Miracle-dz/UniFAR-FTUs huggingface dataset:
Thesis Materials : Knowledge-based Methods for Identification of Functional Modules in Protein Interaction Networks

The majority of the current methods for identifying modules in protein interaction networks are based solely on analysing topological features of the networks. In contrast, the main idea that underpins the planned thesis is that combining topological information with knowledge about protein function will result in more biologically plausible modules than using approaches based solely on topology. We here propose approaches that use a combination of domain-specific knowledge, derived from Gene Ontology, and topological properties, to generate functional modules from protein interaction networks. By using yeast two hybrid (Y2H) interactions from /S/. /Cerevisiae/ and knowledge in terms of Gene Ontology (GO) annotations, we have elucidated functional modules of interacting proteins. In this report, a summary of the proposed approaches is presented. The methods with the same rationale but slightly different designs have been implemented, tested and evaluated. The first approach, where we combine clusters of proteins based on their mutual neighbours profiles with the corresponding clusters based on GO semantic similarity profiles, treats each of the aspects (functional knowledge and topology) separately to obtain functional clusters, and thereafter merges the clusters into one single structure. In contrast, the other approaches integrate both aspects from the beginning. The two other approaches are two versions of a method named SWEMODE (Semantic WEights for MODule Elucidation), which uses knowledge-based clustering coefficient to identify network modules. The first one is uses the original protein interaction graph, and the second one is a recently designed extension of SWEMODE where the /k/-cores of the graph are emphasised. We demonstrate that all three methods are able to identify the key functional modules in protein interaction networks. The first method was applied to smaller well-studied networks, that are known to contain modules of signalling pathways, while SWEMODE was applied on a large network containing 2 231 proteins and 6 379 interactions. The methods were also used to study intermodule connections, which is a step towards revealing a higher order hierarchy between modules. In this report, we describe and discuss the proposed approaches, along with their strengths and weaknesses. We also propose further extensions and improvements of the proposed methods, some of which may be attempted as the final steps in the implementation phase of the dissertation
Bullet Retarding Forces in Ballistic Gelatin by Analysis of High Speed Video

Abstract : Though three distinct wounding mechanisms (permanent cavity, temporary cavity, and ballistic pressure wave) are described in the wound ballistics literature; they all have their physical origin in the retarding force between bullet and tissue as the bullet penetrates. If the bullet path is the same, larger retarding forces produce larger wounding effects and a greater probability of rapid incapacitation. By Newton's third law, the force of the bullet on the tissue is equal in magnitude and opposite in direction to the force of the tissue on the bullet. For bullets penetrating with constant mass, the retarding force on the bullet can be determined using frame by frame analysis of high speed video of the bullet penetrating a suitable tissue simulant such as calibrated 10% ballistic gelatin. Here the technique is demonstrated with 9mm NATO bullets, 32 cm long blocks of gelatin, and a high speed video camera operating at 20,000 frames per second. It is found that different 9mm NATO bullets have a wide variety of potential for wounding and rapid incapacitation. This technique also determines the energy transfer in the first 15 cm and/or first 30 cm of tissue, which are important parameters in estimating the probability of rapid incapacitation in some of the ARL/BRL models. This method predicts that some 9mm bullets have a much higher probability of rapid incapacitation than others and the rank ordering of bullet effectiveness is in agreement with other studies.
Survivability of probiotics under hostile conditions as affected by prebiotic-based encapsulating materials

ABSTRACT Prebiotics-based encapsulation aids in improving the structure of microbeads and the survivability of probiotics. The current study focused on the exploration of a prebiotic-based encapsulation system (alginate-inulin) to improve the viability of probiotics under in vitro and carrier food. Probiotic (L. acidophilus) was encapsulated by the ionotropic gelation method. Microbeads with inulin inclusion were found to be compact and smooth with the highest encapsulation efficiency (98.87%) among the rest of the treatments. Alginate-inulin-based microbeads showed the highest count (8.41log CFU) as compared to other treatment as well free cells under simulated gastrointestinal conditions. Furthermore, alginate-inulin encapsulation maintained recommended (107–108 log CFU/ml) probiotic viability in carrier food throughout the storage period. Probiotic encapsulation aids in controlling the post-acidification of the carrier product (yogurt). The results of this study indicated that the alginate-inulin-based encapsulation system has promising potential to ensure the therapeutic number of probiotics in vitro as well in carrier foods.
On the causality and plausibility of treatment effects in operations management research

Empirical research in operations management (OM) has made rapid strides in the last 30 years, and increasingly, OM researchers are leveraging methods used in the econometrics and statistics literature to assess the causal effects of interventions. We discuss the two key challenges in assessing causality with observational data (i.e., baseline bias, differential treatment effect bias) and how dominant identification approaches such as matching, instrumental variables, regression discontinuity, difference‐in‐differences, and fixed effects deal with such challenges. We surface the key underlying assumptions of different causal estimation methods and discuss how OM scholars have used these methods in the last few years. We hope that reflecting on the plausibility and substantive meaning of underlying assumptions regarding different identification strategies in a particular context will lead to a better conceptualization, execution, evaluation, dissemination, and consumption of OM research. We conclude with a few thoughts that authors and reviewers may find helpful in their research as they engage in discourse related to causality.
Phosphorus and Nitrogen Yield Response Models for Dynamic Bio-Economic Optimization : An Empirical Approach Sihvonen

Nitrogen (N) and phosphorus (P) are both essential plant nutrients. However, their joint response to plant growth is seldom described by models. This study provides an approach for modeling the joint impact of inorganic N and P fertilization on crop production, considering the P supplied by the soil, which was approximated using the soil test P (STP). We developed yield response models for Finnish spring barley crops (Hordeum vulgare L.) for clay and coarse-textured soils by using existing extensive experimental datasets and nonlinear estimation techniques. Model selection was based on iterative elimination from a wide diversity of plausible model formulations. The Cobb−Douglas type model specification, consisting of multiplicative elements, performed well against independent validation data, suggesting that the key relationships that determine crop responses are captured by the models. The estimated models were extended to dynamic economic optimization of fertilization inputs. According to the results, a fair STP level should be maintained on both coarse-textured soils (9.9 mg L−1 a−1) and clay soils (3.9 mg L−1 a−1). For coarse soils, a higher steady-state P fertilization rate is required (21.7 kg ha−1 a−1) compared with clay soils (6.75 kg ha−1 a−1). The steady-state N fertilization rate was slightly higher for clay soils (102.4 kg ha−1 a−1) than for coarse soils (95.8 kg ha−1 a−1). This study shows that the iterative elimination of plausible functional forms is a suitable method for reducing the effects of structural uncertainty on model output and optimal fertilization decisions.
On certain Konhauser and Laguerre matrix polynomials

In this paper, we generalize the well-known Laguerre and Konhauser matrix polynomials, given by Shehata (12), varma and Tas (14), respectively, and we also introduced a set of new Laguerre matrix polynomials \(L_n^{(B,C)} (α,x)\), we also obtained some generating relations and integral representations for these sets of polynomials.
Zero-field spin splitting in modulation-doped AlxGa1−xN∕GaN two-dimensional electron systems

Low-temperature magnetotransport measurements were performed on AlxGa1−xN∕GaN two-dimensional electron systems. By studying the beating pattern in the Shubnikov–de Haas oscillations in a perpendicular magnetic field, we are able to measure the zero-field spin-splitting energies in our systems. Our experimental results demonstrate that the Rashba term due to structural inversion asymmetry is the dominant mechanism which gives rise to the measured zero-field spin splitting in our wurzite AlGaN∕GaN structures. By utilizing the persistent photoconductivity (PPC) effect, we are able to increase the carrier density n in our AlGaN∕GaN two-dimensional electron system. It is found that the Rashba spin-orbit splitting parameter α decreases with increasing n. We suggest that the formation of long-lived electron-hole pairs induced by the PPC effect decreases the large electric field near the AlGaN∕GaN interface, causing α to decrease with increasing n.
Using Desalinated Water for Irrigation: Its Effect on Field Scale Water Flow and Contaminant Transport under Cropped Conditions

Pollution of groundwater by nitrate originating from irrigated fields was considered for this study. We hypothesized that under cropped conditions, low-salinity irrigation water (e.g., desalinated water) could reduce nitrate leaching below the root zone, due to two possible mechanisms: (i) decreased vertical water fluxes and (ii) increased nitrogen uptake by plant roots due to chloride–nitrate competition. The main goal of this study was to investigate this hypothesis. Considering a citrus grove, the investigation relied on three-dimensional (3-D) simulations of flow and transport in a variably saturated and spatially heterogeneous flow domain performed for three successive years. Results of the analyses suggest that the main mechanism responsible for the reduction in the nitrate leached below the root zone under irrigation with low-salinity water is the effect of the latter on the spatial distribution of the rate of water uptake by the roots. The latter, in turn, significantly reduces water content, hydraulic conductivity, and vertical velocity, and, consequently, solute mass fluxes along the soil profile. On the other hand, chloride–nitrate interaction has only a relatively small effect on the nitrate mass fluxes at relatively deep soil depths, far below the root zone, particularly when the irrigation water salinity decreases.
Use of Patient-Reported Data within the Acute Healthcare Context: A Scoping Review

Patient-reported outcome measures (PROMs), patient-reported experience measures (PREMs) and patient satisfaction surveys provide important information on how care can be improved. However, data collection does not always translate to changes in practice or service delivery. This scoping review aimed to collect, map and report on the use of collected patient-reported data used within acute healthcare contexts for improvement to care or processes. Using JBI methods, an extensive search was undertaken of multiple health databases and trial registries for published and unpublished studies. The concepts of interest included the types and characteristics of published patient experience and PROMs research, with a specific focus on the ways in which data have been applied to clinical practice. Barriers and facilitators to the use of collected data were also explored. From 4057 records, 86 papers were included. Most research was undertaken in North America, Canada or the UK. The Hospital Consumer Assessment of Healthcare Providers and Systems tool (HCAHPS) was used most frequently for measuring patient satisfaction. Where reported, data were applied to improve patient-centred care and utilization of health resources. Gaps in the use of patient data within hospital services are noticeable. Engaging management and improving staff capability are needed to overcome barriers to implementation.
Place of residence and time of day as factors affecting the course of vaginal delivery.

INTRODUCTION AND OBJECTIVE Childbirth is one of the most important events in a woman's life and is influenced by many factors. The aim of the research was to analyze the impact of the place of residence of women giving birth and the time of day on the course of natural birth. MATERIAL AND METHODS The study was conducted using the method of analysis of retrospective electronic documentation of patients who gave natural vaginal birth in the St. Zofia hospital in Warsaw, Poland. The analysis covered the period from 1 January 2015-31 December 2020; from 40,007 cases, 20,980 were qualified for final analysis. Analysis of the documentation allowed to obtain the following data: socio-demographic, lifestyle, obstetrics, course of delivery and the condition of the newborn. Analysis of the relationship between qualitative variables was performed using the Chi-square test, while the Mann-Whitney U test was used to compare two quantitative variables. RESULTS Women giving vaginal delivery from rural areas were younger (30.9 vs. 31.3), had primary education (2.4% vs. 1.7%) and secondary education (16.2% vs. 10.1%), were in a relationship (86.1% vs. 81.6%) and more often had a higher BMI at birth (27.8 vs. 27.0), compared to the patients living in cities (p<0.05). In addition, between 07:00-18:59. , induction of labour (20.7% vs. 19.1%), epidural anesthesia (35.4% vs. 34.0%) and episiotomy were performed more often (29.1% vs. 27.8%) (p<0.05). CONCLUSIONS Differences were shown in the course of vaginal delivery in relation to the place of residence of the women, and the time of day of the delivery. These factors should be considered in the planning of perinatal care. At the same time, it is necessary to conduct further research on the analyzed aspect in order to ensure the highest quality care.
Flight results of a 25000-foot-per-second reentry experiment using microwave reflectometers to measure plasma electron density and standoff distance

four- frequency microwave reflectometer having an electron density measurement range from approximately 1010 to 1013 electrons/cm3. Good correlation exists between the reflectometer- determined plasma values and those obtained from electrostatic probes and other flight data taken during this experiment. Measured and computed plasma electron densities in the nose region generally agree except
Effect of General Anesthesia Maintenance with Propofol or Sevoflurane on Fractional Exhaled Nitric Oxide and Eosinophil Blood Count: A Prospective, Single Blind, Randomized, Clinical Study on Patients Undergoing Thyroidectomy

Background: Nitric oxide (NO) is considered a means of detecting airway hyperresponsiveness, since even non-asthmatic patients experiencing bronchospasm intraoperatively or postoperatively display higher levels of exhaled NO. It can also be used as a non-invasive biomarker of lung inflammation and injury. This prospective, single-blind, randomized study aimed to evaluate the impact of two different anesthesia maintenance techniques on fractional exhaled nitric oxide (FeΝO) in patients without respiratory disease undergoing total thyroidectomy under general anesthesia. Methods: Sixty patients without respiratory disease, atopy or known allergies undergoing total thyroidectomy were randomly allocated to receive either inhalational anesthesia maintenance with sevoflurane at a concentration that maintained Bispectral Index (BIS) values between 40 and 50 intraoperatively or intravenous anesthesia maintenance with propofol 1% targeting the same BIS values. FeΝO was measured immediately preoperatively (baseline), postoperatively in the Postanesthesia Care Unit and at 24 h post-extubation with a portable device. Other variables measured were eosinophil blood count preoperatively and postoperatively and respiratory parameters intraoperatively. Results: Patients in both groups presented lower than baseline values of FeΝO measurements postoperatively, which returned to baseline measurements at 24 h post-extubation. In the peripheral blood, a decrease in the percentage of eosinophils was demonstrated, which was significant only in the propofol group. Respiratory lung mechanics were better maintained in the propofol group as compared to the sevoflurane group. None of the patients suffered intraoperative bronchospasm. Conclusions: Both propofol and sevoflurane lead to the temporary inhibition of NO exhalation. They also seem to attenuate systemic hypersensitivity response by reducing the eosinophil count in the peripheral blood, with propofol displaying a more pronounced effect and ensuring a more favorable mechanical ventilation profile as compared to sevoflurane. The attenuation of NO exhalation by both agents may be one of the underlying mechanisms in the reduction in airway hyperreactivity. The clinical significance of this fluctuation remains to be studied in patients with respiratory disease.
Cardiorespiratory Fitness and the Risk of All-Cause, Cardiovascular and Cancer Mortality in Men with Hypercholesterolemia

Abstract Background: Whether higher cardiorespiratory fitness (CRF) confers protection against cardiovascular disease (CVD) in individuals with manifest hypercholesterolemia is poorly understood. Methods: Participants were 8920 men aged 20–82 years with hypercholesterolemia but no history of CVD and/or cancer and who received a preventive examination at the Cooper Clinic in Dallas, TX, USA, during 1974–2001. CRF was quantified as maximal treadmill test duration and was grouped for analysis as low, moderate, or high based on the traditional Aerobics Center Longitudinal Study cutpoints. Using Cox regression analyses, we computed hazard ratios and 95% confidence intervals for risk of mortality based on CRF. Results: During an average of 17 years of follow-up, 329 CVD and 290 cancer deaths occurred. After control for baseline age, examination year, body mass index, total cholesterol, smoking, alcohol intake, physical activity, hypertension, diabetes, and parental history of CVD, hazard ratios (95% confidence interval) for CVD deaths across moderate and high categories of CRF (with low fit as referent) were: 0.66 (0.50–0.87) and 0.55 (0.39–0.79), respectively. There was an inverse association between CRF and CVD death among normal-weight (trend p < 0.0001), younger (<60 y, trend p = 0.01), and inactive men (trend p = 0.002). However, no significant association was found between CRF and cancer mortality. Conclusions: Among men with hypercholesterolemia, higher CRF was associated with a lower risk of dying from CVD independent of other clinical risk factors. Our findings underscored the importance of promoting CRF in the primary prevention of CVD in patients with hypercholesterolemia.
Understanding how nutrient limitation and plant traits influence carbon in mangrove‐seagrass coastal ecosystems

Mangrove forests and seagrass meadows provide critical ecosystem services, including the accumulation of “blue carbon. ” Plants' functional traits could influence this blue carbon accumulation. To test for interactions among functional traits and blue carbon accumulation, we conducted a study in connected mangrove‐seagrass coastal ecosystems in southeast Florida (USA). We quantified how plants' above‐ground traits correlated with sediment nutrient content, and how changes in traits along inland‐to‐coastal gradients influenced inorganic and organic carbon storage potential. Physical traits of Thalassia testudinum were higher at sites with higher sediment phosphorus (SP) and nitrogen (SN) concentrations. Sediment organic carbon concentrations were positively correlated to T. testudinum physical traits. Root density, pneumatophore abundance, specific leaf area, leaf toughness, leaf nitrogen, and phosphorus content were positively correlated with SN concentrations in the mangrove forest coastal fringe. Mangrove leaf thickness and root complexity index were negatively correlated with SP concentrations in the coastal fringe. Our results also indicate that seagrass above‐ground traits and blue carbon were strongly correlated in areas with higher sediment nutrient concentrations. Moreover, mangrove root complexity is coupled with phosphorus limitation, whereby highly complex root systems develop with decreasing phosphorus concentrations. Distinct functional traits of plants drive variation in carbon retention capacity even in interconnected ecosystems.
HUBUNGAN PENGETAHUAN DAN PERSEPSI MASYARAKAT DENGAN UPAYA PENCEGAHAN COVID-19 DI KELURAHAN SRONDOL WETAN, SEMARANG

A case of pneumonia with no known cause was found in Wuhan City, Hubei Province, China in December 2019. Until finally, the samples studied showed the etiology of the new coronavirus named Coronavirus Disease-2019 (COVID-19). This virus can be transmitted from human to human and has spread widely in China and more than 190 countries and including Indonesia. Data from the Health Office show that in the Srondol Wetan sub-district, Semarang City has the highest positive cases of COVID-19 in the Banyumanik sub-district, with 11 confirmed positive cases. This study aims to identify the relationship between public knowledge and perceptions with efforts to prevent COVID-19 in the Srondol Wetan Village, Semarang. This type of research is analytical research with a quantitative approach. The population in this study were the people of Srondol Wetan village with a sample of 120 people who were taken by purposive sampling technique. Collecting research data using a questionnaire via Google form, then analyzed using the Spearman statistical test. The results of analysis showed that there was a significant relationship between the knowledge variable and the efforts to prevent COVID-19 with p-value = 0.000. Then there is a significant relationship between perceptions and efforts to prevent COVID-19, p-value = 0.045 in Srondol Wetan Village, Semarang. The conclusion of the study is that there is a significant relationship between knowledge and perception and efforts to prevent COVID-19.
‘EMI is like a durian’: Chinese students’ perspectives on an ideal English-medium instruction classroom in higher education

Abstract This paper reports a qualitative study of what constitutes an ideal EMI classroom from the perspective of university students. Data were collected through in-depth interviews with 26 university students from various disciplines at a large public university in China. The analysis reveals three core themes, which were perceived to be integral to an ideal EMI classroom: 1) an integration between content, language, and learning strategies, 2) a process-oriented course design permeated with a translanguaging approach, and 3) moving beyond specific EMI classrooms with a future and community orientation. This paper argues that EMI needs to be approached as a full educational experience with multiple dimensions (i.e. cognitive, social, and affective), through which, students gradually build up their professional knowledge and disciplinary literacy as well as foster their sense of belonging and direction in their situated subject field.