jimnoneill/paper-to-field-training huggingface dataset:
A study on the use of search engines for answering clinical questions

Field: Health Professions (Health Sciences)

This paper describes an evaluation of the answerability of a set of clinical questions posed by physicians. The clinical questions belong to two categories of the five-leaf high-level hierarchical Evidence Taxonomy created by Ely and his colleagues: Intervention and Non Intervention. The questions are passed to two search engines (PubMed, Google), two questionanswering systems (MedQA, Answers.com’s Brain-Boost), and a dictionary (OneLook) for locating the answers to the question corpus. The output of the systems is judged by a human and scored according to the Mean Reciprocal Rank (MRR). The results show the need for question modification and analyse the impact of specific types of modifications. The results also show that No Intervention questions are easier to answer than Intervention questions. Further, generic search engines like Google obtain higher MRR than specialised systems and even higher than a version of Google based on specialised literature (PubMed) only. In addition, an analysis of the location of the answer in the returned documents is provided.
Protein Kinase Cβ Coordinates Dopamine Transporter and Dopamine Autoreceptor Signaling

Field: Neuroscience (Life Sciences)

Dopamine (DA) neurons contain dopamine transporters (DAT) and presynaptic D2 dopamine receptors (D2DR), which inhibit DA exocytosis and increase DAT trafficking to the plasmalemmal membrane upon agonist stimulation. Using PKCβ−/− mice, we find that protein kinase Cβ (PKCβ) regulates constitutive and stimulated DAT trafficking plus D2DR activities: PKCβ reduces D2DR-controlled DA exocytosis, but enhances the ability of D2DRs to increase DAT trafficking. Because PKCβ phosphorylates D2DR, which may increase receptor internalization, we hypothesize that lack of PKCβ will enhance D2DR surface localization. Radioligand binding and immunoflorescence labeling experiments were performed to determine surface localization of D2DR and DAT following treatment with the specific PKCβ inhibitor LY379196. Inhibition of PKCβ significantly increased the surface localization of D2DR in both assays but had no effect on DAT surface levels. Our results indicate that PKCβ facilitates D2DR and DAT coupling. In the absence of PKCβ activity, the coupling between D2DR and DAT is lost, as seen by the discoordination between D2DR and DAT. This work was supported by NIH grants DA011697, DA007267, and GM07767.
A novel role of Rad26 in dynamic chromatin disassembly during transcriptional elonagtion in vivo

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Cockayne Syndrome group B (CSB) is a DNA dependent ATPase in human, and plays an important role in transcription as well as transcription‐coupled repair (TCR). Mutations in CSB gene lead to cockayne syndrome (CS) charaterised by many traits reminiscient of normal aging. Deciphering the molecular roles of CSB is, thus, essential for disease management and understanding the causes of general aging and related ailments. However, the precise in vivo modes of action of CSB in regulation of transcription and TCR are not yet clearly understood. In this study, we show that the yeast homologue (Rad26) of CSB specifically associates with the coding regions of transcriptionally active genes, and promotes association of elongating RNA polymerase II (RNAPII). However, Rad26 does not control the recruitment of initiating RNAPII or formation of the pre‐initiation complex at the promoter. Intriguingly, we also find that Rad26 enhances the eviction of histone H2A‐H2B dimer, but not histone H3‐H4 tetramer, from the coding regions of active genes. These results, together, demonstrate for the first time the distinct function of Rad26 in promoting specific eviction of histone H2A‐H2B dimer during transcriptional elongation. This work was supported by Mallinckrodt Foundation.
Role of mathematical modeling in low-level radioactive waste management

Field: Environmental Science (Physical Sciences)

With increased experience in shallow land burial of radioactive wastes, there is general recognition of the need for improved practices to reduce the release of radioactivity to the biosphere. One approach is to use mathematical models to gain insights into the impact of possible preventive and corrective engineering measures. Two deterministic models of hydrologic processes have been examined. On a watershed scale, a unified hydrologic model has been applied to the White Oak Creek Watershed in Oak Ridge, Tennessee. Comparison of predicted and observed streamflow at the basin outlet are favorable. The model has been applied to evaluate the consequences of a disposal area development, operation, and management; including clear-cutting of forested areas, installing near-surface infiltration-reduction seals, and surface water diversion channels. On a localized scale, a near-surface infiltration-reduction seal has been studied using a finite-element model for subsurface flow. The model has been used to calculate spatial moisture content and velocity distributions near the seal. Model results show how the path of infiltrating rainwater is altered. 7 figures.
A Combined QM/MM Poisson−Boltzmann Approach

Field: Chemistry (Physical Sciences)

A method of solving the mixed quantum mechanical/molecular mechanical (QM/MM) Hamiltonian in solution, using the Poisson-Boltzmann (PB) equation to calculate partial charges and solvation free energies, is presented. This method combines a linear scaling divide and conquer semiempirical algorithm with the PB equation in a QM/MM framework, allowing only a specified region's charges to be polarized by the solvent while using fixed charges from a MM force field for the remaining system. This can save time over a full QM implementation, only requiring self-consistency to be achieved in a small QM region, while giving comparable results. The solvation free energy of pentapeptides capped with an acetyl group (ACE) at the N-terminus and an N-methylamine group at the C-terminus (NME) was used to study the accuracy of this method as well as several small protein systems. The solvation free energies for the QM/MM implementation compare well with a full QM treatment of the same system, giving reasonable representations for the solvation free energy of the entire system independent of the QM region's size. In the case of the pentapeptides, the average error was only 4.9 kcal/mol with the smallest QM region. This mixed method will allow an accurate description of solvation effects in an area of interest, such as an active site, using mixed QM/MM Hamiltonians. Possible applications for this method include protein-ligand binding and reaction mechanism studies.
The choice of methods for estimating the losses and the development of software models for the evaluation of electromagnetic accessibility of radio monitoring

Field: Engineering (Physical Sciences)

The results of the analysis of using verified the International Telecommunication Union methods of calculating the sygnal attenuation and/or field strength on the route propagation software products, designed to assess the availability of electromagnetic radio-electronic means of various purpose wideband radio monitoring. The comparative analysis of results of calculation with the results of experimental studies. Figs.: 4. Refs.: 9 titles.Keywords: electromagnetic availability of radio monitoring; signal attenuation; the field strength; radio monitoring.
Forecasting the Impact of the Structure of Financing Sources on the Results of Production Activity in Agriculture

Field: Arts and Humanities (Social Sciences)

The study conducted to assess the impact of the source of financing on the results of production activities of small and medium-sized businesses in agriculture in Kazakhstan is presented in the article. When building the model, the authors used the method of correlation and regression analysis, including calculations of pairwise regression, as well as the method of building statistical equations. Statistical data on the volume of financing of SMEs in agriculture by way of own funds, government resources (concessional lending, subsidies, and leasing), and non-state sources of financing such as borrowed funds from banks, microfinance organizations, credit partnerships, and leasing companies were used as the factors. Firstly, the results of the study showed that such factors as bank lending and leasing financing by private companies do not have a significant impact on production volumes. Secondly, of all the factors analyzed, the greatest impact on gross output was made by financing by microfinance organizations and credit partnerships, which determines and indicates the need for the development of non-state sources of financing. Thirdly, a comprehensive approach combining state financial support as well as available non-state financial resources is needed to achieve the strategic objectives of economic development and ensure the required level of food security.
DEEP BRAIN STIMULATION: 20 YEARS AFTER

Field: Neuroscience (Life Sciences)

Life is electricity. Living cells have a potential difference across their membranes, which can be changed by applying an electrical current. Therefore the functional activity of neurons and their connections inside circuits are subject to alterations by electrical stimulation. Deep Brain Stimulation (DBS) has been developped after the advancement in stereotactic neurosurgery. The first indication of DBS was applied to intractable pain almost half a century ago. In 1987, the discovery of DBS in movement disorders by the Grenoble team led by A.L. Benabid marked the start of this wide scale procedure. The initial idea was to decrease bilateral thalamotomyinduced morbidity in the treatment of tremors, thanks to the functional nature of DBS, which enables adjustement and reversibility of electrical parameters. Spatial adjustability was also possible with the development of quadripolar electrodes. The discovery at the origin of the antitremor effect of DBS was its dependence on the frequency of stimulation: no effect at 50 Hz, possible worsening at lower frequencies, improvement at higher frequencies with a plateau reached over 130 Hz. Changes in voltage influence the spatial spreading of current around the stimulation contact, whereas pulse width has minimal effect. From this discovery was born the concept of electrical neuromodulation of brain tissue. The high frequency effect, which mimics that of lesioning has been discovered for brain nuclei other than the thalamus, namely the globus pallidus (GP) and subthalamic nucleus (STN). These latter targets have been stimulated following the advancement in basal ganglia pathophysiology in the 90s, when it has been be shown that the parkinsonian akinesia is associated with subthalamo-pallidal hyperactivity in animal models of Parkinson disease. Afterwards, the extension of the indications and stimulated targets stemed from clinical observations of secondary effects of DBS in Parkinson disease, such as the antidyskinetic effect in the GPi or the beneficial effect of obsessive compulsive disorder in the STN. This sounded the start of DBS in various types of dyskinesias, mainly dystonia and psychosurgery. So far, DBS is a therapy world-wide validated and regularly applied as the surgical procedure of choice for various types of tremors (parkinsonian, essential and symtomatic of a brain lesion) in the Vim thalamus or the subthalamic region, for the motor complications of levodopa-responsive Parkinson diseases in the STN or GPi and for primary dystonia in the GPi. The type of surgery by far the most frequently used is bilateral STN stimulation in Parkinson disease with about 50 000 operated patients. As any powerful therapy, the indications and patient management should
Biological and Ecological Observation of Rasbora sp. for Conservation and Domestication Purpose in Lake Ie Sayang

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Lake Ie Sayang provides habitat to several variety of aquatic animals including small fish such as Rasbora sp. However, their existences in nature are increasingly decline due to overfishing and degradation of its natural habitat. The objective of this study was to investigate some habitat characteristics, biological and ecological aspects of bileh fish ( Rasbora sp.). Water quality parameters were recorded in situ and fish samples were collected from the water in four stations during April to July 2021. Fish sex ratio and body length-weight were measured ex situ. The data are presented in table and analyzed descriptively. The result revealed that this fish was mainly found at station 1. This station is characterized by the presence of several aquatic plants as feeding ground and fish sanctuary. This fish was easy to find in the mid-water level to water surface and near the land. The water quality parameters revealed that the temperature was in the range 30.2°C to 31.9°C, pH 6.13 to 6.35, DO 3.0 mg/l to 5.25 mg/l, and transparency 47 cm to 58 cm. Fish sex ratio showed that the overall number of females was higher than males with the average range of fish body length-weight were 34.05 mm to 41.33 mm and 1.25 g to 1.58 g respectively.
Business Communications and Cultural Specifics in the Behavior of Generation Z

Field: Business, Management and Accounting (Social Sciences)

Abstract: Nowadays recruitment is very competitive. Different companies publish their job ads online on a daily basis, using various channels and strategies. Using a marketing approach to recruitment allows segmentation and strategic targeting. Business communication has become an important tool for a successful recruitment campaign. Targeting the message to Generation Z requires knowledge of their “average Joe”. Using business communication tools as well as knowledge about cultural differences and dimensions and successful intercultural communication can guarantee relevant and suitable activities to involve capable representatives of Generation Z during the recruiting process. Creating the right message in the job advertisement can attract the best candidates. This article presents results from empirical research on what Generation Z finds attractive in a workplace. 282 people are interviewed using the Minnesota Satisfaction Questionnaire. The results show Generation Z values social service, creativity, the manager’s technical knowledge, authority and compensation. Using those factors as key words in the job advertisement can result in both attracting the right candidates and reducing recruitment costs. The research is done in a Bulgarian cultural environment. Key words: business communications, advertisement message, recruiting, generation Z, values, work environment.
Pathogenetic variants of sepsis in oncologicy practice

Field: Medicine (Health Sciences)

Introduction Over the past 30 years, sepsis has been an urgent interdisciplinary problem of modern medicine due to the increase in morbidity and a consistently high mortality rate. Patients of oncological hospitals have a high predisposition to the development of sepsis, both in the postoperative period and in the departments of chemo and radiation therapy. In addition, sepsis may be a complication of the postoperative period in patients undergoing surgical treatment. Of interest is not only the clinical and laboratory diagnosis of sepsis in this category of patients, but also the features of its morphological picture, due to uniform diagnostic criteria. The greatest difficulties arise in the study of autopsies, after antitumor chemotherapy, which causes a secondary immunodeficiency condition characterized by the absence of a classical morphological picture of sepsis. The use of modern antibacterial drugs, as well as pathogenetic therapy of sepsis also leads to its pathomorphosis, which also complicates diagnosis. The aim of the study is to systematize the literature data and the results of our own research on the features of morphological manifestations of sepsis in oncological pathology, depending on cancer treatment. Material and methods The search and selection of literary sources was carried out in PubMed, GoogleScholar, electronic library systems elibrary.ru, the search depth is 30 years. Results and Discussion Sepsis in cancer patients after surgical interventions is characterized by hyperergic type of tissue reactions with hyperplasia of lymphoid and myeloid tissue and classic manifestations of septicopyemia of varying severity of purulent metastatic process: from macroscopically distinguishable abscesses to mini-foci of purulent inflammation. Against the background of antibiotic therapy, there is a pathomorphosis of sepsis with a predominance of microcirculation disorders and small focal ulcers. In patients after chemotherapy, accompanied by leukopenia and agranulocytosis, with sepsis, hypoplasia of myeloid and lymphoid tissue is noted, and in the internal organs, along with microcirculation disorders, foci of necrosis, severe dystrophic changes with the absence of neutrophil infiltration are found. Conclusion Sepsis in cancer patients from pathogenetic positions is heterogeneous, depending on the characteristics of the body and the nature of treatment, it should be divided into hyper- and anergic. The diagnosis of sepsis is clinico-morphological, which requires not only the use of clinical and laboratory diagnostic scales, but also the definition of criteria for morphological diagnosis.
5-HT activates nitric oxide-generating neurons to stimulate chloride secretion in guinea pig distal colon

Field: Medicine (Health Sciences)

The participation of nitric oxide (NO) in serotonin (5-hydroxytryptamine; 5-HT)-evoked chloride secretion in guinea pig distal colon was examined. Submucosal/mucosal segments were mounted in Ussing flux chambers, and an increase in short-circuit current ( I sc ) was used as an index of secretion. Addition of 5-HT to the serosal side produced a concentration-dependent (10 −7 –10 −5 M) increase in I sc caused by chloride secretion. N G -nitro-l-arginine (l-NNA) significantly reduced the 5-HT-evoked early (P-1) and late (P-2) responses to 61.1 and 70.6% of control, respectively. Neurally evoked response was also inhibited by l-NNA. The NO donor sodium nitroprusside (SNP, 10 −4 M) increased basal I sc mainly because of chloride secretion. The SNP-evoked response was significantly reduced by tetrodotoxin but was unchanged by atropine or indomethacin. These results suggest that the 5-HT-evoked increase in I sc is associated with an NO-generating mechanism. Atropine significantly reduced the 5-HT (10 −5 M)-evoked P-1 and P-2 responses to 71.8 and 19.7% of control, respectively. Simultaneous application of atropine andl-NNA further decreased the 5-HT-evoked responses more than either drug alone; application ofl-NNA and atropine decreased the 5-HT-evoked P-1 and P-2 responses to 68.5 and 39.2% of atropine-treated tissues, respectively. These results suggest that noncholinergic components of P-1 and P-2 responses are 71.8 and 19.7% of control, respectively, and that NO components of P-1 and P-2 responses are 32 and 61%, respectively, of the noncholinergic component of the 5-HT-evoked responses. The results provide evidence that NO may participate as a noncholinergic mediator of 5-HT-evoked chloride secretion in guinea pig distal colon.
Left atrial shape predicts recurrence after atrial fibrillation catheter ablation

Field: Medicine (Health Sciences)

Abstract Introduction Multiple markers left atrium (LA) remodeling, including LA shape, correlate with outcomes in atrial fibrillation (AF). Catheter ablation is an important treatment of AF, but better tools are needed to determine which patients will benefit. In this study, we use particle‐based modeling to quantitatively assess LA shape, and determine to what degree it predicts AF recurrence after catheter ablation. Methods and results There were 254 patients enrolled in the DECAAF study who underwent cardiac magnetic resonance imaging of the LA prior to AF ablation and were followed for recurrence for up to 475 days. We performed particle‐based shape modeling on each patient's LA shape. We selected shape parameters using the LASSO method and factor analysis, and then added them to a Cox regression model, which included multiple clinical parameters and LA fibrosis. We computed Harrell's C‐statistic with and without shape in the model. We used the model to stratify patients into recurrence risk classes by both shape and shape and fibrosis combined. Three shape parameters were selected for inclusion. The C‐statistic increased from 0.68 to 0.72 when shape was added to the model (P < 0.05). Visualized shapes showed that a more round LA shape with a shorter, more laterally rotated appendage was predictive of recurrence. Conclusion LA shape is an independent predictor of recurrence after AF ablation. When combined with LA fibrosis, shape analysis using PBM may improve patient selection for ablation.
Can young children make active choices? Outcomes of a feasibility trial in seven‐year‐old children

Field: Health Professions (Health Sciences)

This project evaluated the feasibility of a child-centred 24-week physical activity intervention. The Play5 strategy encourages children to choose to play vigorously five times a day for about as long as school recess. The seven-year-old children were randomised to control (n = 176) or intervention groups (n = 132). Data were collected at baseline and post-intervention. Programme evaluation included parent questionnaire, teacher records and a seven-day pedometer record with a subsample of children. The programme was successful in increasing vigorous activity (p = 0.04), but did not impact on moderate or sedentary activities. Young children were able to choose to be active without parent or teacher direction.
Hamartoma affecting ampullary electroreceptors and epitheliotropic lymphoma in a captive electric eel Electrophorus varii

Field: Veterinary (Health Sciences)

Few reports are available describing lesions in captive electric eels Electrophorus spp. This report describes 2 types of cutaneous proliferative lesions (i.e. hamartoma and neoplasm) in a captive electric eel. Ampullary electroreceptor hamartomas appeared grossly as 2 discrete, smooth, pink, spherical, cutaneous masses measuring 6 and 18 mm in diameter. Histologically, hamartomas were composed of predominately spindle cells that were separated into lobules by a peripheral rim of polygonal cells. Spindle cells were arranged in vague streams and occasionally whorls within a myxomatous matrix. Polygonal cells arranged in variably sized trabeculae and cords within a pre-existing fibrovascular stroma surrounded the streams of spindle cells. Admixed with the polygonal cell population were multiple mucous glands and alarm cells, similar to those seen in normal regions of epidermis. Histochemical stains confirmed similar components in the normal ampullary electroreceptor as in the hamartomas. Lymphoma was also present, appearing grossly as patchy pitting, erythematous, and thickened areas of the skin affecting the entire animal. Lymphoma was diffusely infiltrating and expanding the epidermis, oral mucosa, and branchial mucosa up to 1.5 mm in thickness. It was composed of an unencapsulated, well-demarcated, moderately cellular neoplasm composed of lymphocytes arranged in small dense sheets and clusters that separated and effaced epidermal cells. This is the first report of lymphoma in an electric eel, and the first report of ampullary electroreceptor hamartoma in any animal species.