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Development of a LAMP simulation and selection pipeline to predict primer success
No full textBackground: The loop-mediated isothermal amplification (LAMP) technique is widely used in research and diagnostics, yet its underlying mechanisms remain poorly understood. Methods: The experiment utilized 31 synthetic gene templates (500-560 base pairs) from the 16S rRNA V8 region of bacterial phyla, paired with specific primer sets (F3, FIP, BIP, B3) individually designed for template amplification. Wet lab amplification experiments were conducted at 68°C for 120 minutes using 105 template molecules per reaction, and were validated using 1.2% agarose gel electrophoresis. Dry lab amplification was predicted using our model data and analysis for LAMP-process pipeline. Predictions centered on assessing dumbbell and ladder formation near the 3’ end of primer sequences. SeqKit software facilitated 1512 condition explorations, with evaluations of primer sensitivity, specificity, accuracy, and F1 values. Results: Predictive LAMP amplification experiment yielded mixed results, suggesting some primer issues. Six primer sets displayed consistent amplification across templates. We identified two models with optimal conditions based on F1 scores exceeding 0.64, highlighting the balance between sensitivity and specificity. Parameters like oligomer length and mismatch tolerance have significantly influenced predictive accuracy. Conclusion: This novel LAMP prediction model can enhance primer design and promote more LAMP applications
The Banyera Practice: An Assessment of Unloading Practices and Fish Handling Techniques at the Navotas Fish Port Complex, NCR, Philippines
No full textWhile fish ports ensure the efficiency of the supply chain in the Philippines, most of the regional fish ports still lack functional cold storage facilities (Manalili et al., 2015); hence, the most usual technique of fish preservation in landing sites is through banyera practice — the use of basins filled with crushed ice for the fish quality preservation. However, this traditional method increases the risk of contaminating fish when no proper sanitary measures are taken (Allende et al., 2020). As such, fish ports also become a focal point for the increasing postharvest losses, estimated at 25-40% of total fish production, due to mishandling brought about by contamination (DA-BFAR, 2018).
The Navotas Fish Port Complex (NFPC) is the largest in the country and in Southeast Asia, regulated by the Philippine Fisheries Development Authority. It receives the most number of unloaded catch amounting to approximately 293,431 MT annually. From 2020 to 2023, it is estimated that 17% of the total volume of fish unloaded and traded in Navotas Fish Port Complex is subjected to quality losses. This study determined the nature of food safety management in NFPC, more specifically the unsafe practices inside market halls where fish were exposed to safety hazards during the critical stages of postharvest activities such as (1) unloading, (2) fish grading, and (3) trading. Specifically, the researcher intended to (1) present the worker profile and the nature of unloading and fish handling practices, (2) enumerate the food safety management practices in market halls, (3) examine the dimensions of food safety culture (FSC), (4) analyze the gap between managers and workers perception regarding FSC, (5) evaluate the level of compliance of NFPC in certain food safety standards, and (7) recommend strategies to enhance the food safety culture in market halls.
The respondents of the study were composed of 120 manual workers (batilyo, lagum, kargador) and the managers of the Food Safety and Environmental Management Unit and Market Division Unit in NFPC selected through convenience sampling; data were collected through a printed survey questionnaire. This study used descriptive and quantitative research design to provide a more comprehensive overview of the area\u27s workflow with measures of central tendency, sign test, and cross-tabulation methods as the tools for data analysis. Majority of the respondents of the study are the batilyos (37.5%) - the workers responsible for dragging the banyera to respective stalls using a tub puller who also serves as helper of the auctioneer in sorting the fish in terms of its type and size. For the worker profile, the study revealed that the average age of manual workers in NFPC is 28 years old, with a range spanning from 16 to 66 years old. All of them are male and a large portion of the respondents has been in the field for 1 to 5 years and most of them are high school undergraduates (47.50%).
Results showed that the three major operations inside a market hall are unloading, fish grading, and trading. Market 1 is responsible for fishing vessel unloading, Market 2 is for overland unloading, and Market 3 is for fishing boat unloading. About 206 MT per day are unloaded in Market 1, 92 MT for Market 2, and 48 MT for Market 3. Fish grading involves classification into first class (primera), second class (segunda), and third class (tersera) by technical enumerators based solely on visual inspection guided by a quality standard scheme. The trading practice is facilitated by fish brokers and auctioneers through a whisper-bidding system, selling fish per banyera and per kilo. From the survey responses, this study revealed that the precautionary measures taken by manual workers in the major operations are subpar, with lapses including failure to change melted ice, usage of unclean banyera, and fish sorting on unclean floors, which are clearly food safety violations based on the food safety manual issued by the PFDA.
In terms of food safety management practices, this study revealed that these were subdivided into: (1) inspection procedure, (2) quality assurance, (3) storage conditions, and (4) hygiene and sanitation. Findings of unsafe practices have shown that the NFPC does not have any food safety certification at present. Additionally, there is no specific food safety training given for the manual workers. Furthermore, their traceability system for incoming products inside the fish port is only applicable to Market 1 and Market 2. Other findings revolve around non-compliance of workers which are focused on improper attire, smoking while working, unregulated placement of banyeras, littering, and inadequate cleaning substances to be used.
For the dimensions of food safety culture, it indicated that communication is currently the most prioritized dimension within the Navotas Fish Port Complex, followed by the worker-unit commitment. The suggests effective information flow from management to workers and a strong sense of responsibility among workers regarding food safety practices. Conversely, the least prioritized dimensions were identified as environment, risk, and management - highlighting areas needing attention to enhance food safety culture. Moreover, there is misalignment of dimensions of food safety vulture between workers and managers in terms of management, commitment, and environment which suggests the need to implement corrective measures.
In addition, the Navotas Fish Port Complex have shown a 59.09% compliance rate with the Code of Hygienic Practice for the Sale of Fresh Agriculture and Fishery Products (PNS 46:2006). Despite efforts to maintain cleanliness, issues such as poor storage conditions and inconsistent water and ice quality compromise fish quality. For ISO 22000:2018 certification, the compliance rate is 58.33%. While systems like self-audits, a food safety manual, and an organizational structure are in place, there are gaps in product quality verification and periodic reviews of food safety protocols. With this level of compliance and the mentioned practices at present, around 21% of fish unloaded experienced quality loss due to spoilage, damage, defects, impurities, and undesirable sizes. This resulted in a financial loss of approximately Php 176,731 over a 15-day period starting in March, the peak season. This assessment excludes some seafood varieties, indicating potential for further losses.
Overall, the unloading practices and fish handling techniques impact food safety culture through their influence on the prevention of contamination, adherence to hygiene protocols, and maintenance of product quality standards. Hence, recommendations given were focused on enhancing facilities and equipment, fish quality control, and dimensions of food safety culture tailored to management, manual workers, and for future researchers. Pursuing ISO 22000:2018 certification, stricter enforcement of hygiene standards along with biosecurity measures for pest control, and site design improvement are recommended for an enhanced food safety culture. Finally, for future researchers, investigating what are the potential drivers for non-compliance of workers and management can provide additional insights on how to address the root cause of the problem and eventually, finding ways on how to improve worker\u27s efficiency towards food safety in the fisheries sector
Household Vulnerability Assessment to Flooding in Barangay Sta. Ana, Mateo, Rizal
No full textThis paper assesses the vulnerability to flooding of households in a select barangay in the Philippines. Being one of the most vulnerable countries to climate change impacts, it is predicted that increased precipitation and rainfall events would likely lead to increased flooding in the country. Assessing vulnerability is important to identify who is vulnerable in the community and what are the sources of their vulnerability. The study adopted the definition of vulnerability as a function of exposure, sensitivity, and adaptive capacity. Key informant interviews and focus group discussions were conducted to identify the hazards in the community. Data was collected from 108 households in the low-lying areas of Barangay Sta. Ana. To analyze the data, multi-criteria analysis (MCA) and vulnerability as expected poverty (VEP) were utilized to calculate a vulnerability index. MCA was used to measure how households scored in every dimension of vulnerability. The VEP method was also employed to gain an econometric measure of using the three- step feasible generalized least squares procedure (FGLS). Vulnerability defined was defined as the likelihood the household will fall below the poverty threshold. The results of the study showed that the majority of households in Brgy. Sta. Ana was not vulnerable to flooding. Results of the MCA show that 74 out of 108 households were not vulnerable to flooding. Among the vulnerable households, common characteristics were poverty, low diversified income, and low social capital. Similarly, results of the VEP procedure showed that 61 of 105 households were not likely to fall into poverty in the future. Results further revealed that highest flood height, household size, number of income sources, and educational attainment of household head significantly affect consumption at household level
The Effects of Remittances and Education on Energy Consumption in the Philippines
No full textThis study examined the effects of remittances and education on energy consumption in the Philippines. By performing diagnostic tests, unit root tests, and cointegration analysis, it analyzed the effects of remittance and education on energy consumption with the control variables of economic growth, energy prices, and trade. The results indicated that real GDP and trade openness increase energy consumption in the Philippines in the long-run while energy prices reduce energy consumption in the Philippines in the long run. The results suggest however that remittance and education in the Philippines have no short-run or long run relationship with energy consumption. The study used Autoregressive Distributive Lag (ARDL) to verify the short-run and long-run dynamics among the variables. The study specified the implications of the findings for policy directions and areas for future studies
Effects of redrying methods on the milling potential, crude protein and total phenolic content, and antioxidant activity of stored inorganic and organically-grown paddy
No full textThis study sought to determine the effects of redrying techniques (no redrying or Control, 2-h, 4-h, and 6-h redrying with stirring every 30 min, Farmer\u27s Practice or 6-h redrying with one stirring) on grain quality of stored inorganic and organic paddy rice as well as the redrying method that gives the best quality rice. PSB Rc82 rice harvested in October 2016 was used in the experiment conducted in February 2017. Quality parameters evaluated were moisture content, brown rice, total milled rice, crude protein content in percent, total phenolic content, and 2-2 diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity. PSB Rc82 paddy exposed to various redrying techniques had moisture contents ranging between 9.10% – 11.60% moisture content (wet basis) (MCw.b.). Brown rice (70.19% – 72.52%), total milled rice (66.37% – 69.12%), crude protein content (6.60% – 7.73%), total phenolic content (0.0783 – 0.0950 mg g-1 GAE), and % DPPH radical scavenging activity (19.53 – 26.87) of PSB Rc82 rice were all significantly influenced by redrying process and type of rice (p = 0.05). The 2-h redrying produced maximum brown and milled rice recoveries while removing the least amount of moisture from paddy samples. Control (no redrying) had the highest crude protein content. Inorganic rice had more crude protein and was more nutrient-dense than organic rice. Samples dried at 4-h redrying with 30-min stirring intervals produced the highest % DPPH radical scavenging activity. Moreover, DPPH radical scavenging activities were higher in inorganic rice than in organic rice. Variations between inorganically and organically-grown rice in terms of crude protein content and antioxidant activity with different redrying methods may be attributed to crop management. Findings from this study can help other researchers in determining the best redrying method to attain maximum grain quality and health benefits important to consumers
Exponential regression analysis programming and application.
No full textRegression equations involving nonlinear parameters can easily be solved by using iterative calculation as presented by Williams. For these equations, exact significance tests are not possible, but the predicting equation will usually yield best approximates of the observed values whenever the model chosen is suited to the data. An over—all test of the regression can be done through the analysis of variance. The method of iterative calculation will provide rapid estimation of the parameters, if convergence is attainable. In some cases, only a few cycles of iteration may be sufficient to give the required value of the parameters to be used in fitting the curve to the data
A Study on the Transportation of an Incorporated Association to a Cooperative: Maprotas, Inc. to Maprotas Agriculture Cooperative (MAC) in Tayabas City, Quezon
No full textCooperative had been introduced to be an answer to the traditional constraints and vulnerabilities that smallholder farmers experience in the Philippines as a means to improve the sustainability of producing agricultural products and enhancing profits and competitiveness. There are 21 categories of cooperatives that were listed in the Republic Act 9520, an act creating the Cooperatives Development Authority (CDA) and in Memorandum Circular 2015-05, the category of agricultural cooperative is added. It is defined as, a primary cooperative whose members, cultivate plants, animals, fungi, and other living organisms for economic purposes, and aims to empowers these individuals by organizing and benefiting from the current government and industry landscape, such as exemption from tax, reduction of fees, the benefits of bulk purchasing, and group farming between its members. Cooperatives are categorized not only by type but also by size or the value of their assets. Cooperatives are categorized not only by type but also by size or the value of their assets. The criteria for classification are as follows: micro cooperatives with assets up to Php 3 million, small cooperatives with assets between Php 3 million and 15 million, medium cooperatives with assets over Php 100 million. As of November 14, 2023, there are a total of 20,072 cooperatives in the Philippines, and in more recent times, with as many as 27 types of cooperatives listed, namely Advocacy, Agrarian Reform, Agriculture, Consumers, Cooperative Bank, Credit, Dair, Education, Electric, Federation-Secondary, Labor Service, Marketing, Multipurpose, Producers, Service, Small Scale Mining, Technology Service, Transport, Union-Secondary, Union-Tertiary, Water Service, and Workers.
This study entitled A Study on the Transformation of an Incorporated Association to a Cooperative: Maprotas, Inc. To Maprotas Agriculture Cooperative (MAC) in Tayabas City, Quezon was conducted to provide insights in the organization\u27s decision to convert from a non-stock, non profit corporation association registered under the Securities Exchange Commission (SEC) into an agricultural cooperative under the CDA (Cooperative Development Authority). This specially aims to: (1) Present the profile of MAC as an non-stock, non profit cooperative. (2) Map the timeline of events that led to the organization\u27s decision to convert the non-stock corporation to a cooperative structure. (3) Identify the factors and considerations that triggered and motivated the decision to convert the non-stock corporation to a cooperative structure. (4) Compare the effects and changes to the organization performance experienced as a non-stock corporation and as a cooperative. (5) Formulate recommendations based on findings and insights on the organization\u27s decision to convert to a cooperative structure.
With the organizational profile of both structure of non-stock corporation and cooperative presented, it gives a perspective to identify any triggers or motivations for the decision to transform the organization to a cooperative which included the Five Capital Key Indicators of Adaptive (Social, Financial, Human, Natural, Physical), looking at the timeline of events and identifying notable points of interests that had affected the decision, the Key Elements of the McKinsey 7-S Model (Structure, Strategy, System, shared Values, Skill, Style, Staff), and lastly an analysis on both the environmental and internal elements of the organization as well as other barriers, difficulties, factors and considerations. Afterwards, a comparison of the effects and changes brought about by the decision that the organization experienced, such as its organizational performance and financial performance is analyzed and see if there are significant reason for it to have affected the decision and the organization. With the information gathered, it is put through a balanced scorecards that aims to analyze and measure performance of the organization in the four perspectives (Financial, Customers, Internal Business Process, Growth and Learning), which gives further insight into both financial and nonfinancial perspectives. After getting the given score based on the key performance measures and its respective values, further findings give more information on its strengths and weaknesses that it should address. Thus, giving recommendations actions to be taken and to be considered for the organization\u27s strategic planning and for its development and growth.
In the form of tax exemptions and incentives, the organization benefited from the transformation. Tax exemptions are a notable benefit for cooperatives as they receive more than just being a corporation. This led to more financial freedom toward the organization\u27s goals and purpose and funds for more projects and ventures to develop value-adding products and services to generate surplus profits. The pre-membership seminars enhanced the selection process in a way wherein it screens and gives a more thorough and selective approach to accepting members in the organization, providing more committed and engaged members in the long run and fostering a better sense of belonging in the cooperative. In terms of membership, the shift also introduced financial incentives for members, encouraging greater participation, investment, and motivation. The establishment of more committees with straightforward responsibilities, along with clearly defined goals and purposes in the by-laws and articles, suggests a more organized and structured approach to the cooperative\u27s operations. This contributed to better decision-making and overall effectiveness. Better government support and promotion gave the organization a more favorable environment to grow, allowing the cooperative to gain a market reach larger than its previous position as a non-stock corporation. There is also increased coordination with the Cooperative Development Authority (CDA) compared to the last engagement with the Securities and Exchange Commission (SEC), indicating a shift towards aligning with entities specifically focused on supporting and regulating cooperatives. This change resulted in more appropriate assistance and guidance for the organization.
A balanced scorecard provided a framework to measure performance from four perspectives, covering both financial and nonfinancial perspectives namely: Financial, Customer, Internal business processes, and Growth and learning. These measurements calculated the achivement of strategic objectives, and was based on the 1) Understanding the visions and missions described in cooperative objectives, 2) Understanding the relationship between selected strategic objectives, and 3) Analyzing measurements employed in selected strategic objectives. The Insights dervied from the financial perspective was that Gross Margin and Total Asset Turnover Ratio would indicate that there is some success in managing costs and asset utilization but failed to pass In regards to a Return On Asset, Return on Equity, and Operating Margin. In the customer perspective, serving Its members, It had also not had gained a score, and needed reassess its strategies to enhance member benefits and satisfaction. For Internal Business Processes, active participation of members has shown positive results, indicating engagement and attendance from the organization\u27s members. The membership process needs improvement in providing in-depth knowledge or at least having regular review sessions to keep members up-to-date or knowledgeable. Product development and infrastructure improvement have positive scores, showcasing successful initiatives being taken with the procurement of new assets as well as adding new value-added products. Lastly, In
Growth and Learning, positive scores in the frequency of participation in educational training and seminars, member development, and member satisfaction highlight the cooperative\u27s commitment to continuous learning and member well-being. The cooperative has strengths in member engagement, certain product initiatives, and educational activities. However, challenges exist in financial performance, customer benefits, and certain aspects of internal processes. Addressing these challenges will be crucial for the cooperative\u27s sustained success during the transformation. Based on these, some insights on how to address these are: (1) Implement strategies to improve financial metrics, focusing on ROA, ROE, and Operating Margin, (2) Reassess and enhance strategies to increase the distribution of net surplus to members, (3) Strengthen the membership process by providing more in-depth knowledge during pre-membership seminars, (4) Continue successful initiatives in product development and infrastructure improvement, (5) Maintain a proactive stance in educational training and seminars while addressing specific member suggestions for an increased net profit surplus.
The transformation of Mangosteen Producers of Tayabas Association, Inc. (MAPROTAS, Inc.) into Maprotas Agriculture Cooperative (MAC) represents a strategic shift aimed at enhancing the organization\u27s sustainability and effectiveness. Leveraging the McKinsey 7S Model and the Balanced Scorecard framework, MAC should focus on enhancing its democratic structure through regular educational workshops to deepen members\u27 understanding of cooperative governance principles and processes. Additionally, a targeted strategy is needed to improve MAC\u27s financial performance, with a focus on increasing profitability metrics such as ROA, ROE, and Operating Margin through cost reduction measures and revenue enhancement strategies. Strengthening MAC\u27s commitment to cooperation, solidarity, and social responsibility is crucial for equitable benefit distribution and member empowerment. Investing in continuous training and development programs will equip stakeholders with the necessary skills in cooperative governance, sustainable agriculture, and community engagement. Implementing transparent and participatory financial management systems and fostering a culture of participatory leadership and transparent decision-making processes are essential. Aligning staff roles and responsibilities with cooperative objectives and prioritizing initiatives aimed at improving financial metrics, enhancing member benefits, and optimizing internal processes will be crucial for MAC\u27s success in its transformation
Consumer Preference and Willingness to Pay for Local Specialty Coffee in the University of the Philippines Los Baños, 2023
No full textThe study was conducted to analyze the consumer preference and willingness to pay for local specialty coffee in the University of the Philippines Los Baños. Specifically, the study aimed to: (1) describe the socio-economic characteristics of coffee drinkers in UPLB; (2) determine the level of knowledge and awareness of coffee drinkers in UPLB toward specialty coffee; (3) compare the preference and willingness to pay for specialty coffee of students and working individuals in UPLB; (4) identify the factors associated with the willingness to pay for specialty coffee; and (5) recommend marketing strategies for specialty coffee based on the results.
Primary data were obtained from 100 respondents who are undergraduate students, faculty, staff, and research representative coffee drinkers in UPLB by providing a questionnaire and conducting a product test. The analytical tools used were descriptive analysis, 5-point Likert scale importance ranking, 9-point hedonic scale, contingent valuation, chi-square test of independence, and Cramer’s V.
Most respondents consumed two 250 mL cups of coffee per day and their usual places of consumption are their homes/apartments/dorm, office/workplace, and coffee shops. Student-respondents have higher budget allocated for coffee compared to the working individuals. Most of the respondents consume coffee for the caffeine or for the purpose to stay awake. Half of the respondents have a moderate knowledge level about specialty coffee. The top three most important attributes that the respondents are looking for in their coffee are as follows in order: flavor, aroma, and price. The important attributes that are associated with the knowledge level of the respondents towards specialty coffee are flavor, fragrance, aroma, and sustainability.
The product test compared three coffee samples: low quality commercial coffee, high quality commercial coffee, and specialty coffee. Using the 9-point hedonic scale, the respondents rated the three samples according to their preference. The test results show that specialty coffee was the least liked out of the three samples. The rating that the specialty got is “neither like nor dislike” which shows a neutral preference towards specialty coffee.
The contingent valuation showed that the majority of respondents are willing to pay for specialty coffee despite the neutral response from the product test. Students have higher willingness to pay compared to working individuals. The chi-squared test of independence showed that the variables that are associated with the respondent’s willingness to pay are purchasing level and place of consumption.
It is recommended to market and increase the coffee consumer’s awareness to coffee to increase their appreciation of specialty coffee. It is important to consider the budget of the consumers in marketing specialty coffee. The best place to consider in marketing specialty coffee is coffee shop. Conducting further studies about specialty coffee is suggested to further improve and highlight the attributes of specialty coffee that the respondents would prefer and can even invite new coffee drinkers
