Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitat use of spring migrating dabbling ducks in the Wabash River Valley, Usa

ABSTRACT Stopover sites provide crucial habitat for waterfowl to rest and refuel during migration. Knowledge of which land-cover types are of greatest importance to migrating waterfowl and how the surrounding landscape influences their use can inform management decisions and conservation plans to adequately meet resource requirements. Specifically, spring migration habitat is essential for waterfowl preparing for breeding yet is an understudied period of the life cycle. We placed radio-transmitters on Mallards (Anas platyrhynchos) and Green-winged Teal (Anas crecca) between January and April 2016–2017 in the Wabash River Valley of Illinois and Indiana to assess habitat use and movement patterns. Both Mallards and Green-winged Teal primarily used emergent and woody wetlands, with 89% of use points in these land-cover types even though they made up <5% of the study area. Use of both dry and flooded row crops was minimal. While habitat selection of Mallards was similar for diurnal vs. nocturnal periods, Green-winged Teal used emergent wetlands at a higher rate during the day and shifted to woody wetlands at night. In general, sites surrounded by greater amounts of open water, upland forest, and upland herbaceous/grassland cover were more likely to be used than areas surrounded by row-crop agriculture. Additionally, private and public lands enrolled in conservation easement programs (such as the Wetlands Reserve Program) were frequently used by migrating waterfowl compared to other protected or public lands. These findings highlight the importance of a landscape-level approach to conservation, specifically focusing on wetland restoration while minimizing reliance on agricultural fields to fulfill habitat needs during spring migration in the Midwest.
Half of Prescribed Antibiotics Are Not Needed: A Pharmacist-Led Antimicrobial Stewardship Intervention and Clinical Outcomes in a Referral Hospital in Ethiopia

Intense antibiotic consumption in Low- and Middle-Income Countries (LMICs) is fueled by critical gaps in laboratory infrastructure and entrenched syndromic management of infectious syndromes. Few data inform the achievability and impact of antimicrobial stewardship interventions, particularly in Sub-Saharan Africa. Our goal was to demonstrate the feasibility of a pharmacist-led laboratory-supported intervention at Tikur Anbessa Specialized Hospital in Addis Ababa, Ethiopia, and report on antimicrobial use and clinical outcomes associated with the intervention. Methods: This was a single-center prospective quasi-experimental study conducted in two phases: (i) an intervention phase (November 2017 to August 2018), during which we implemented weekly audit and immediate (verbal and written) feedback sessions on antibiotic prescriptions of patients admitted in 2 pediatric and 2 adult medicine wards, and (ii) a post-intervention phase (September 2018 to January 2019) during which we audited antibiotic prescriptions but provided no feedback to the treating teams. The intervention was conducted by an AMS team consisting of 4 clinical pharmacists (one trained in AMS) and one ID specialist. Our primary outcome was antimicrobial utilization (measured as days of therapy (DOT) per 1,000 patient-days and duration of antibiotic treatment courses); secondary outcomes were length of hospital stay and in-hospital all-cause mortality. A multivariable logistic regression model was used to explore factors associated with all-cause in-hospital mortality. Results: We collected data on 1,109 individual patients (707 during the intervention and 402 in the post-intervention periods). Ceftriaxone, vancomycin, cefepime, meropenem, and metronidazole were the most commonly prescribed antibiotics; 96% of the recommendations made by the AMS team were accepted. The AMS team recommended to discontinue antibiotic therapy in 54% of cases during the intervention period. Once the intervention ceased, total antimicrobial use increased by 51.6% and mean duration of treatment by 4.1 days/patient. Mean LOS stay as well as crude mortality also increased significantly in the post-intervention phase (LOS: 24.1 days vs. 19.8 days; in hospital death 14.7 vs. 6.9%). The difference in mortality remained significant after adjusting for potential confounders. Conclusions: A pharmacist-led AMS intervention focused on duration of antibiotic treatment was feasible and had good acceptability in our setting. Cessation of audit-feedback activities was associated with immediate and sustained increases in antibiotic consumption reflecting a rapid return to baseline (pre-intervention) prescribing practices, and worse clinical outcomes (increased length of stay and in-hospital mortality). Pharmacist-led audit-feedback activities can effectively reduce antimicrobial consumption and result in better-quality care, but require organizational leadership's commitment for sustainable benefits.
Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2

Antiapoptotic members of B-cell leukemia/lymphoma-2 (BCL-2) family proteins are one of the overexpressed proteins in cancer cells that are oncogenic targets. As such, targeting of BCL-2 family proteins raises hopes for new therapeutic discoveries. Thus, we used multistep screening and filtering approaches that combine structure and ligand-based drug design to identify new, effective BCL-2 inhibitors from a small molecule database (Specs SC), which includes more than 210,000 compounds. This database is first filtered based on binary “cancer-QSAR” model constructed with 886 training and 167 test set compounds and common 26 toxicity quantitative structure-activity relationships (QSAR) models. Predicted non-toxic compounds are considered for target-driven studies. Here, we applied two different approaches to filter and select hit compounds for further in vitro biological assays and human cell line experiments. In the first approach, a molecular docking and filtering approach is used to rank compounds based on their docking scores and only a few top-ranked molecules are selected for further long (100-ns) molecular dynamics (MD) simulations and in vitro tests. While docking algorithms are promising in predicting binding poses, they can be less prone to precisely predict ranking of compounds leading to decrease in the success rate of in silico studies. Hence, in the second approach, top-docking poses of each compound filtered through QSAR studies are subjected to initially short (1 ns) MD simulations and their binding energies are calculated via molecular mechanics generalized Born surface area (MM/GBSA) method. Then, the compounds are ranked based on their average MM/GBSA energy values to select hit molecules for further long MD simulations and in vitro studies. Additionally, we have applied text-mining approaches to identify molecules that contain “indol” phrase as many of the approved drugs contain indole and indol derivatives. Around 2700 compounds are filtered based on “cancer-QSAR” model and are then docked into BCL-2. Short MD simulations are performed for the top-docking poses for each compound in complex with BCL-2. The complexes are again ranked based on their MM/GBSA values to select hit molecules for further long MD simulations and in vitro studies. In total, seven molecules are subjected to biological activity tests in various human cancer cell lines as well as Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) assay. Inhibitory concentrations are evaluated, and biological activities and apoptotic potentials are assessed by cell culture studies. Four molecules are found to be limiting the proliferation capacity of cancer cells while increasing the apoptotic cell fractions.
Streamlining the KOOS Activities of Daily Living Subscale Using Machine Learning

Background: Functional outcome scores provide valuable data, yet they can be burdensome to patients and require significant resources to administer. The Knee injury and Osteoarthritis Outcome Score (KOOS) is a knee-specific patient-reported outcome measure (PROM) and is validated for anterior cruciate ligament (ACL) reconstruction outcomes. The KOOS requires 42 questions in 5 subscales. We utilized a machine learning (ML) algorithm to determine whether the number of questions and the resultant burden to complete the survey can be lowered in a subset (activities of daily living; ADL) of KOOS, yet still provide identical data. Hypothesis: Fewer questions than the 17 currently provided are actually needed to predict KOOS ADL subscale scores with high accuracy. Study Design: Cohort study (diagnosis); Level of evidence, 2. Methods: Pre- and postoperative patient-reported KOOS ADL scores were obtained from the Surgical Outcome System (SOS) data registry for patients who had ACL reconstruction. Categorical Boosting (CatBoost) ML models were built to analyze each question and its value in predicting the patient’s actual functional outcome (ie, KOOS ADL score). A streamlined set of minimal essential questions were then identified. Results: The SOS registry contained 6185 patients who underwent ACL reconstruction. A total of 2525 patients between the age of 16 and 50 years had completed KOOS ADL scores presurgically and 3 months postoperatively. The data set consisted of 51.84% male patients and 48.16% female patients, with a mean age of 29 years. The CatBoost model predicted KOOS ADL scores with high accuracy when only 6 questions were asked (R2 = 0.95), similar to when all 17 questions of the subscale were asked (R2 = 0.99). Conclusion: ML algorithms successfully identified the essential questions in the KOOS ADL questionnaire. Only 35% (6/17) of KOOS ADL questions (descending stairs, ascending stairs, standing, walking on flat surface, putting on socks/stockings, and getting on/off toilet) are needed to predict KOOS ADL scores with high accuracy after ACL reconstruction. ML can be utilized successfully to streamline the burden of patient data collection. This, in turn, can potentially lead to improved patient reporting, increased compliance, and increased utilization of PROMs while still providing quality data.
SquamataBase: a natural history database and R package for comparative biology of snake feeding habits

Abstract Public databases in taxonomy, phylogenetics and geographic and fossil occurrence records are key research tools that provide raw materials, on which broad-scale analyses and synthesis in their respective fields are based. Comparable repositories for natural history observations are rare. Publicly available natural history data on traits like diet, habitat and reproduction are scattered across an extensive primary literature and remain relatively inaccessible to researchers interested in using these data for broad-scale analyses in macroecology and macroevolution. In this paper, I introduce SquamataBase, an open-source R package and database of predator-prey records involving the world’s snakes. SquamataBase facilitates the discovery of natural history observations for use in comparative analyses and synthesis and, in its current form, contains observations of at least 18,304 predator individuals comprising 1,227 snake species and at least 58,633 prey items comprising 3,231 prey taxa. To facilitate integration with comparative analysis workflows, the data are distributed inside an R package, which also provides basic functionality for common data manipulation and filtering operations. Moving forward, the continued development of public natural history databases and their integration with existing digitisation efforts in biodiversity science should become a priority.
Human platelet lysate efficiency, stability, and optimal heparin concentration required in culture of mammalian cells

Background Fetal bovine serum (FBS) has been used to support the growth and proliferation of mammalian cells for decades. Owing to several risk factors associated with FBS, several trials have been conducted to evaluate substitutes to FBS with the same efficiency and the lower risk issues. Methods In this study, human platelet lysate (HPL) derived from activated human platelets was evaluated as an alternative to FBS due to the associated risk factors. To evaluate the efficiency of the preparation process, platelet count was performed before and after activation. The concentrations of several growth factors and proteins were measured to investigate HPL efficiency. HPL stability was studied at regular intervals, and optimal heparin concentration required to prevent gel formation in various media was determined. The biological activity of HPL and FBS was compared by evaluating the growth performance of Vero and Hep-2 cell lines. Results Result of platelet count assay revealed the efficiency of HPL preparation process. Growth factor concentrations in HPL were significantly higher than those in FBS, while the protein content of HPL was lower than that of FBS. Stability study data showed that the prepared HPL was stable for up to 15 months at −20℃. Ideal heparin concentration to be used in different media was dependent on calcium concentration. Results of cell viability assay showed that HPL was superior to FBS in supporting the growth and proliferation of Vero and Hep-2 cells. Conclusion The HPL prepared by the mechanical activation of platelets may serve as an efficient alternative to FBS in cell culture process.
MAP6 is an intraluminal protein that induces neuronal microtubules to coil

MAP6 enters the lumen and induces coiling in a previously unidentified class of neuronal microtubules. Neuronal activities depend heavily on microtubules, which shape neuronal processes and transport myriad molecules within them. Although constantly remodeled through growth and shrinkage events, neuronal microtubules must be sufficiently stable to maintain nervous system wiring. This stability is somehow maintained by various microtubule-associated proteins (MAPs), but little is known about how these proteins work. Here, we show that MAP6, previously known to confer cold stability to microtubules, promotes growth. More unexpectedly, MAP6 localizes in the lumen of microtubules, induces the microtubules to coil into a left-handed helix, and forms apertures in the lattice, likely to relieve mechanical stress. These features have not been seen in microtubules before and could play roles in maintaining axonal width or providing flexibility in the face of compressive forces during development.
Modifications of the Staphylococcus aureus cell envelope and their roles in host-microbe interactions

Peptidoglycan muropeptides, potent proinflammatory components, are amidated in Staphylococcus aureus for unknown reasons. To study whether this modification may modulate proinflammatory capacity, cytokine induction by isogenic S. aureus strains with different amidation levels and by synthetic amidated/nonamidated muramyldipeptides was evaluated. However, amidation did not significantly affect cytokine induction. This finding contributes to defining peptidoglycan receptor specificities and indicates that further rationales for muropeptide amidation have to be considered.
The identification of the mycelia of wood-decay fungi by their oxidation reactions with phenolic compounds

1. For purposes of identification of fungus rnycelia the production of Iaccase and tyrosinase type enzymes in the mycelia of decay fungi is estimated by using several phenolic conlpounds in a droptest. 2. The influence of some factors, as pH, temperature, age of the inycelium and intraspecific variations on the results is shown. 3. On the basis of their production or not of laccase and tyrosinase the mycelia are divided into four groups: 1) producing neither laccase nor tyrosinase, 2) producing only tyrosinase, 3) producing only laccase, 4) producing both laccase and tyrosinase. On the basis of the intensity of the reactions and taking into account the specific reactions with some substances these groups may be subdivided into smaller ones. 4. The results are commented and compared with results obtained by other authors with different methods. 5. The occurrence and characteristics of laccase and tposinase and their possible role in metabolism, especially in lignin degradation, and their action on other phenolic substances is briefly discussed.
Comparison of balance and coordination abilities between asthmatic patients and healthy subjects>

Balance and coordination are important elements of most activities of daily living. Previous Studies have shown that structural defect and deformities develop in the chest wall due to decreased thoracal mobility in asthmatic patients. The biomechanics of the thoracic cage may effect the body’s global mechanics. This situation may cause balance disorder that leads a disorientation in coordination. Therefore, the aim of the study was to compare the balance and coordination between asthmatic patients and healthy individuals. Forty-nine asthma patients(study group) diagnosed according to GINA at Pamukkale University, Medical Faculty, Department of Pulmonary Disease, were included in the study and fifty-one healthy subjects participated as controls. Dynamic balance was assessed with Kinestetic Ability Trainer(SportKAT550). Coordination ability was assesed with finger nose test and toe tapping test. The average age of study group was 35,3±10,3 years; the avarage age of control group was 36,17±8,47 years(p>0,05). When the results belonging to the groups were compared, there were significant difference in SportKAT550 Total dynamic score(p=0,001), finger nose test(p=0,007) and toe tapping test(p=0,003) between the groups. The results of our study showed that there as a decrease in the balance and coordination capabilities of asthmatic patients. We think that factors affecting balance and coordination in asthmatic patients should be searched in further studies. Therefore, balance and coordination should be evaluated in asthmatic patients and added balance and coordination exercises in pulmonary rehabilitation programs.
Correlation of HbA1c with atherogenic index of plasma and endothelial dysfunction in type 2 diabetic subjects

Introduction: Endothelial dysfunction (ED) is a well known initial stage of atherosclerosis and cardiovascular disease (CVD) in general population. Recently studies shown increased HbA1c is a marker for cardiovascular risk in subjects with diabetes and without diabetes. Atherogenic index of plasma (AIP) is another risk factor for cardiovascular events. Hence, the study has been designed to assess the correlation of HbA1c with AIP and ED in type-2 diabetic subjects to forecast risk of cardiovascular events. Materials and Methods: Hundred subjects are enrolled into study with the age of 38 to 58 years, among these 50 were type 2 diabetic subjects and 50 were healthy controls. HbA1c was estimated by immuno-turbidimetric method. Nitric oxide (NO) was measured by kinetic cadmium reduction method and AIP was calculated by standard formula Log (triglyceride/HDL-c). ‘Kruskal Wallis’ test was used to perform statistical variables between the study groups. The association between the variables was executed by “Pearson correlation test”. Result: HbA1c level was shown to be significantly higher in type-2 diabetic subjects than healthy controls. Significant lower level of NO was observed in type-2 diabetic subjects than healthy controls. AIP level was significantly higher in type-2 diabetic subjects than healthy controls. The present study also observed significant correlation of HbA1c with NO and AIP. Conclusion: We have found that HbA1c has significant correlation with NO and AIP. Therefore, estimation of HbA1c may be a predictable marker for cardiovascular events in type-2 diabetic subjects. Keywords: Glycated hemoglobin, Atherogenic index of plasma, Nitric oxide, Cardiovascular disease.
Dynamics of the transcription preinitiation complex in vivo

Transcription by all three eukaryotic RNA polymerases involves the assembly of a large preinitiation complex (PIC) at gene promoters. The PIC comprises several general transcription factors (GTFs) including TBP, and the respective RNA polymerase. It has been suggested that some GTFs remain stably bound at active promoters to facilitate multiple transcription events. By using two complementary approaches we show that, in G1-arrested yeast cells, TBP exchanges very rapidly even at the most highly active RNA Pol II promoters. A similar situation is observed at RNA Pol III promoters. By contrast, TBP remains stably bound at RNA Pol I promoters. We also provide evidence that, unexpectedly, PIC dynamics is neither the cause, nor the consequence, of nucleosome exchange at most of the RNA Pol II promoters we analyzed. These results point to a stable reinitiation complex at RNA Pol I promoters and suggest independent PIC and nucleosome turnover at many RNA Pol II promoters.
Regulation of macronutrient metabolism by the gastrointestinal tract of ruminants

Title of Document: REGULATION OF MACRONUTRIENT METABOLISM BY THE GASTROINTESTINAL TRACT OF RUMINANTS Samer Wassim El-Kadi, Doctor of Philosophy, 2006 Directed By: Assistant Professor Brian J. Bequette, Department of Animals Sciences We set out to test the hypothesis that the gastrointestinal tract (GIT) of ruminant animals catabolizes amino acids (AAs) preferentially. We sought to determine whether this catabolism represents an obligate requirement, and whether this requirement stems from the need to generate energy or support other metabolic demands. The aim was to determine the composition of macronutrients (AAs, short chain fatty acids, and glucose) utilized by the GIT, and the influence of general and specific nutrient supplies on their routes of metabolism. Increasing protein supply to the small intestine did not alter the total amount of glucose removed by the GIT indicating, that glucose removal and therefore utilization is obligatory. In contrast, the net removal of AAs occurred at a constant proportion of arterial and luminal supplies. This translated to larger amounts of AAs removed from blood circulation, and from the lumen of the small intestine in response to increased small intestinal and blood supplies. In this respect, the net absorption of branched chain AAs was, unlike other essential AAs lower than 100%. Further, glutamate and glutamine net appearance across the whole GIT and small intestine was unaffected by protein supply. The disproportionate utilization of BCAA, glutamate, and glutamine as compared to other AAs suggested that their metabolism occurred toward specific metabolic requirements, possibly energy production. When Krebs cycle metabolism was investigated using individual AAs, glucose, and short chain fatty acids, leucine and valine did not contribute to the flux of Krebs cycle intermediates. Conversely, αketoglutarate flux originated mainly from glutamate, and to a lesser extent from glutamine. Though glucose was metabolized to pyruvate and lactate, glucose did not contribute to Krebs cycle intermediates. Overall, these results indicated that glutamate plays an important role in energy metabolism, and in insuring replenishment of Krebs cycle intermediates that leave the cycle via cataplerosis. Yet, the results raised new questions that ought to be addressed in future studies. The fate of glutamine carbon, the metabolic significance of leucine and valine deamination, and the role of glucose partial catabolism to lactate need to be investigated. REGULATION OF MACRONUTRIENT METABOLISM BY THE GASTROINTESTINAL TRACT OF RUMINANTS.