jimnoneill/paper-to-field-training huggingface dataset:
S1557 Ampullary Cancer as an Uncommon Cause of Abdominal Pain

Field: Medicine (Health Sciences)

Introduction: Ampullary cancer is a rare form of cancer originated in the ampulla of Vater, accounting for fewer than 1% of cancers related to gastrointestinal tract. The incidence of ampullary cancer is estimated to be approximately 4-10 cases per million population. Obstructive jaundice is the most common presenting symptom, found in 80% of patients. Other nonspecific symptoms include abdominal pain, fever, nausea, dyspepsia, and GI bleeding from tumor sloughing. Here, we'd like to present a case of an advanced ampullary cancer with abdominal pain as the only major symptom on presentation. Case Description/Methods: 65-year-old female presented with progressively worsening abdominal pain in the epigastric area and bloating for 3 weeks. She also had pale stools during the same period but denied any nausea, vomiting, jaundice, or unintentional weight loss. She is a lifetime non-smoker but uses alcohol occasionally. Initial blood tests were mostly unremarkable except for mildly elevated alkaline phosphatase (ALP) and gamma-glutamyl transferase (GGT). Computed tomography (CT) of the abdomen and pelvis revealed 3 liver lesions in addition to common biliary duct dilatation. Based on imaging results, a lesion in the distal common duct or ampulla causing metastatic disease was suspected. She then underwent endoscopic retrograde cholangiopancreatography (ERCP) and had a double pigtail stent placed in the common bile duct. Also, a large fungating mass in the ampulla was discovered and biopsied. Her symptoms resolved after the procedure and was discharged home. A few days later the ampulla mass was reported to be poorly differentiated invasive adenocarcinoma. Her carcinoembryonic antigen (CEA) level at time of diagnosis was 6.5 ng/mL (normal range: 0-2.5 ng/mL). Discussion: Ampullary cancer is a rare form of malignancy, constituting less than 1% of all gastrointestinal cancers and only 6% of cancers in the periampullary region. Its most common presenting symptom is obstructive jaundice, caused by tumor compression of the distal bile duct. Distinguishing primary ampullary cancer from other periampullary cancers such as cholangiocarcinoma or pancreatic cancer is often difficult. For localized disease, Whipple procedure is the only potentially curative treatment. Due to rarity of the disease, however, there is limited data on treatment choice for advanced ampullary cancer. Combination therapy with gemcitabine and cisplatin appears to confer the best survival advantage.
FIGURE 2. Anthracites zebra Hebard, 1922 in New species and taxonomic notes of Agraeciini from Mount Malindang (Philippines: Mindanao) (Tettigoniidae: Conocephalinae: Agraeciini)

Field: Agricultural and Biological Sciences (Life Sciences)

FIGURE 2. Anthracites zebra Hebard, 1922 male left tegmina (A–D) and stridulatory files (E–H) in ventral views. Scale bars: 2 mm (A–D), 0.5 mm (E–H)
Comparison, Analysis, and Molecular Dynamics Simulations of Structures of a Viral Protein Modeled Using Various Computational Tools

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

The structural analysis of proteins is a major domain of biomedical research. Such analysis requires resolved three-dimensional structures of proteins. Advancements in computer technology have led to progress in biomedical research. In silico prediction and modeling approaches have facilitated the construction of protein structures, with or without structural templates. In this study, we used three neural network-based de novo modeling approaches—AlphaFold2 (AF2), Robetta-RoseTTAFold (Robetta), and transform-restrained Rosetta (trRosetta)—and two template-based tools—the Molecular Operating Environment (MOE) and iterative threading assembly refinement (I-TASSER)—to construct the structure of a viral capsid protein, hepatitis C virus core protein (HCVcp), whose structure have not been fully resolved by laboratory techniques. Templates with sufficient sequence identity for the homology modeling of complete HCVcp are currently unavailable. Therefore, we performed domain-based homology modeling for MOE simulations. The templates for each domain were obtained through sequence-based searches on NCBI and the Protein Data Bank. Then, the modeled domains were assembled to construct the complete structure of HCVcp. The full-length structure and two truncated forms modeled using various computational tools were compared. Molecular dynamics (MD) simulations were performed to refine the structures. The root mean square deviation of backbone atoms, root mean square fluctuation of Cα atoms, and radius of gyration were calculated to monitor structural changes and convergence in the simulations. The model quality was evaluated through ERRAT and phi–psi plot analysis. In terms of the initial prediction for protein modeling, Robetta and trRosetta outperformed AF2. Regarding template-based tools, MOE outperformed I-TASSER. MD simulations resulted in compactly folded protein structures, which were of good quality and theoretically accurate. Thus, the predicted structures of certain proteins must be refined to obtain reliable structural models. MD simulation is a promising tool for this purpose.
Investigating the Kuan Kreng Peat Swamp Forest using Electrical Resistivity and Ground Penetrating Radar for Carbon Stock Estimation

Field: Environmental Science (Physical Sciences)

Peatlands, also known as bogs, fens, and especially peat swamp forests in tropical regions, are wetland ecosystems where peat layers are present due to anoxic conditions. Immense amounts of carbon are stored in peat layers, making it an important carbon sink for atmospheric carbon and playing a major role in carbon cycle. These peat layers are vulnerable to becoming a carbon emission source due to the disturbance of the peat layer by natural and anthropogenic processes. Southern Thailand comprises several peatlands that have encountered degradation due to cultivation and forest fires, especially the Kuan Kreng peat swamp forest, which is the second largest peatland in Thailand and serves for carbon storage. To evaluate the impact of peatland degradation, carbon stock estimation is necessary; thus, the thickness and distribution of the peat layers are necessary. This study utilizes ground penetrating radar and electrical resistivity imaging, along with conventional core studies, to investigate physical and chemical characteristics and also delineate peat layer.Significant relationships between chemical and physical properties of the peat layer are represented, which is useful for geophysical interpretation. The resistivity profiles show a high resistivity response, in the range of 21.9 to 145.0 ohm-m, which is interpreted as peat layers in the shallow subsurface. The high amplitude, contorted to sub-parallel reflection from GPR profiles, represents a peat layer that has a relatively lowest velocity with the highest dielectric constant. In order to evaluate carbon stock, average values of bulk density (0.19 g/cm&#173;3) and TOC (31.18 wt. %) from the drilling core samples are advocated, resulting in 59.24 Kg C/m3 of carbon density. Then the peat layer average thickness of 18.00 cm from the geophysical survey and core samples are used to estimate the carbon stock per unit area. Therefore, considering the entire area of the Kuan Kreng peat swamp forest, the carbon stock is estimated at a minimum of 7.53 Mt.
Effects of Extraction Solvents on the Total Phenolic Content, Total Flavonoid Content, and Antioxidant Activity in the Aerial Part of Root Vegetables

Field: Agricultural and Biological Sciences (Life Sciences)

The present study aimed to investigate the total phenolics, total flavonoids, and antioxidant activity in terms of the DPPH scavenging, reducing power, and H2O2 scavenging of the aerial parts of onion, white radish, red radish, carrot, and beet as affected by different extraction solvents. Generally, the aerial part of these vegetables has high antioxidant properties. Samples were extracted with methanol (100 and 70%), ethanol (100 and 70%), and water. Total phenolic content was highest when the samples were extracted using 100% methanol, while extraction with 100% ethanol yielded the highest total flavonoids. The highest DPPH activity and H2O2 scavenging values were obtained by extraction of the aerial plant parts with 70% ethanol, and the 70% methanol extract had the highest reducing power. Partial least regression (PLS) was performed to validate the optimum solvent for extraction of the antioxidants and their activity in each plant. The PLS indicated that there was a variation in the validation of the different extracts for each plant. The high antioxidant capacity of root vegetables, which is natural, indicates that they may have health and dietetic advantages for consumers.
Low Complexity Named-Entity Recognition for Indonesian Language using BiLSTM-CNNs

Field: Computer Science (Physical Sciences)

Named-Entity Recognition (NER) is a fundamental task in Natural Language Processing (NLP) and information extraction. NER is used to extract information such as names of the people, organizations, and places. NER has been used in many fields of work, one of which is in chatbot development. NLP and machine learning approaches enable a smarter chatbot with better personal analysis to users. This research builds a NER model in Indonesian Language using Bidirectional Long Short-Term Memory (BiLSTM) and Convolutional Neural Networks (CNNs) model architecture. Unlike the former research, this model only uses word-level embedding in the CNNs layer to keep the model simple. The Named-Entities (NEs) used in this study are limited to the name of the person, organization, location, quantity, and time using the BILOU labeling format. The performance of the model built is measured using micro-averaged f1 score evaluation metric. The BiLSTM-CNNs + pretrained word2vec embedding model provides good performance compared to other models with an f1 score of 71.37%.
Is the accuracy of preoperative MRI stage in rectal adenocarcinoma influenced by tumour height?

Field: Medicine (Health Sciences)

Aim: To our knowledge, no prior studies have addressed the possible effects of tumour height on the accuracy of preoperative magnetic resonance imaging (MRI)-based staging relative to postoperative histopathological assessments in patients with adenocarcinoma of the rectum (RC). This study aimed to investigate whether the accuracy of preoperative MRI stage in RC is influenced by tumour height. Methods: A total of 489 consecutive RC patients scheduled for curative treatment between 2009 and 2013 were included. Of the 489 patients, 133 patients had preoperative chemoradiotherapy (CRT), and 356 patients underwent primary surgery. Low, mid and high RC were defined as a tumour <5 cm, 5–10 cm and >10 cm from the anal verge, respectively. Diagnostic MRI and, for patients with CRT, re-staging MRI features including tumour T-stage (mrT), distance between the tumour border and the distance to the mesorectal fascia (mrMRF), extramural tumour depth (mrEMD), extramural vascular invasion (mrEMVI) and nodal involvement (mrN) were correlated with the corresponding postoperative histopathological findings. Results: There were 115, 186 and 188 patients with low RC, mid RC and high RC, respectively. For all patients, the correlations between mrT and pT and between mrMRF and pCRM were not influenced by tumour height. None of the correlations between mrEMD, mrEMVI and mrN and the corresponding postoperative histopathological findings significantly differed for tumours of different heights. For patients with CRT, a remarkable proportion with low RC were overstaged as ymrT3 compared to ypT0-2. Conclusions: The ability to preoperatively use MRI to accurately stage is not influenced by tumour height. For patients with preoperative CRT, low RC may be MRI overstaged due to post-radiation fibrosis. We found that mrEMD predicts pEMD reliably and should therefore be considered in treatment decisions. Although new MRI techniques are emerging, preoperative RC staging remains incompletely definitive in daily clinical practice.
Monitoring of Measurement Reliability in Power Systems on the basis of Statistical Decision Theory

Field: Decision Sciences (Social Sciences)

The paper considers the monitoring problem of measurement reliability in power systems applying a semantic method of limiting values. Critical analysis of the existing approach to optimization of the decision making boundaries which is based on the Bayes criterion is given in the paper. It is proposed to use a minimax criterion which makes it possible to solve the optimization problem under the conditions of initial uncertainty in the notions of gross error and unreliability of measurements. Values of eiToneous decisions of the 1st and 2nd kinds are specified by taking into account random measurement errors and substitution of the unreliable measurement results.
In the Academy, Data Science Is Lonely: Barriers to Adopting Data Science Methods for Scientific Research

Field: Social Sciences (Social Sciences)

Data science has been heralded as a transformative family of methods for scientific discovery. Despite this excitement, putting these methods into practice in scientific research has proven challenging. We conducted a qualitative interview study of 25 researchers at the University of Michigan, all scientists who currently work outside of data science (in fields such as astronomy, education, chemistry, and political science) and wish to adopt data science methods as part of their research program. Semi-structured interviews explored the barriers they faced and strategies scientists used to persevere. These scientists quickly identified that they lacked the expertise to confidently implement and interpret new methods. For most, independent study was unsuccessful, owing to limited time, missing foundational skills, and difficulty navigating the marketplace of educational data science resources. Overwhelmingly, participants reported isolation in their endeavors and a desire for a greater community. Many sought to bootstrap a community on their own, with mixed results. Based on their narratives, we provide preliminary recommendations for academic departments, training programs, campus-wide data science initiatives, and universities to build supportive communities of practice that cultivate expertise. These community relationships may be key to growing the research capacity of scientific institutions.Â
Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes

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

It is well established that the variable binding-site architecture and composition of the P450 metabolizing heme proteins are major modulators of substrate and product specificity. Even the three closely related human liver isozymes, CYP2C9, CYP2C18, and CYP2C19, do not share all substrates and do not always lead to the same preferred hydroxylation products. The lack of knowledge of their three-dimensional (3D) structures has hindered efforts to understand the differences in their specificities. Building on previous work for the CYP2C9 enzyme, 3D models of CYP2C18 and 2C19 have been constructed and validated by computational methods developed and tested in our laboratory. They were used to characterize explicit enzyme–substrate complexes using the isoform-specific substrates progesterone and (S)-mephenytoin for 2C19 and 2-[2,3-dichloro-4-(3-hydroxypropyloxy)benzoyl]thiophene for 2C18. The results allowed both common and unique binding-site residues to be identified in each model. The calculated preferred hydroxylation site was obtained for each substrate and was found to be consistent with experimental observation. Comparisons were made among the 2C9, 2C18, and 2C19 model binding sites to investigate the subtle differences among them. These models can be used as structure-based guides for mutagenesis studies and screening of potential pharmaceuticals or toxins. Proteins 1999;37:204–217. ©1999 Wiley-Liss, Inc.
Novel Inflammatory Signaling via Interleukin‐13 Decreases Potassium Channel Expression and Increases Vascular Smooth Muscle Excitability

Field: Medicine (Health Sciences)

The transcriptional repressor element‐1 (RE1) silencing transcription factor (REST), also known as neuron‐restrictive silencer factor (NRSF) is a gene silencing transcription factor, which has been characterized as a master regulator of the neuronal phenotype. REST plays a key role in the development of the nervous system and is a critical player in the etiology of neurodegenerative diseases such as Huntington's Disease, though little is known about the role of REST in non‐neuronal cells. We are exploring a potential role of REST as a mediator between inflammation and changes in smooth muscle phenotype. Kv7.5 voltage‐dependent potassium channels, encoded by the KCNQ5 gene, are expressed in smooth muscle cells where they play an important role in determining resting membrane potential. Interleukin‐13 (IL‐13) is an inflammatory cytokine, which is implicated as a primary mediator of the phenotypic changes induced by allergic inflammation in many tissues. In the present study, we hypothesized that IL‐13 can increase nuclear REST and decrease KCNQ5 mRNA expression and Kv7.5 protein in vascular smooth muscle cells, providing a potential link between inflammation, REST and potassium channel‐mediated vascular hyper‐responsiveness. In support of this hypothesis, using A7r5 rat aortic smooth muscle cells, we found that 1) IL‐13 treatment significantly increased nuclear REST, and 2) significantly suppressed the expression of KCNQ5 and Kv7.5 currents, resulting in increased sensitivity of A7r5 cells to arginine vasopressin (AVP). 3) REST overexpression also significantly decreased Kv7.5 currents, and 4) significantly increased the sensitivity of A7r5 cells to AVP. We conclude that inflammation that induces IL‐13 may increase nuclear REST levels and thereby decrease KCNQ5 expression and Kv7.5 currents, ultimately increasing vascular smooth muscle cell excitability and contributing to vascular hyper‐responsiveness. Support or Funding Information The project described was supported by Award Number I01BX007080 from the Biomedical Laboratory Research & Development Service of the VA Office of Research and Development. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Fluvial form in modern continental sedimentary basins: Distributive fluvial systems: COMMENT

Field: Earth and Planetary Sciences (Physical Sciences)

[Weissmann et al. (2010)][1] discuss what they term “distributary fluvial systems” (DFS) to address a key question in the earth sciences: what modern systems are appropriate analogues to the rock record? They conclude “Since DFSs dominate depositional patterns in all continental sedimentary
Commodity Exchanges in Structure of Energy Market: a Fresh Look

Field: Economics, Econometrics and Finance (Social Sciences)

The paper offers a systematized and updated view of exchange-traded energy products. The increase in natural gas and electricity trade volumes at commodity exchanges has dramatically changed the wholesale market structure in Europe. Nowadays commodity exchanges have played an essential role in energy trading. The complexity of exchange technologies and the reasons for their demand are often hidden under everyday exchange routine. Academic analysis of exchange activity has traditionally been feebly developed, because, firstly, classical economics assumes that finding of equilibrium between supply and demand is an instantaneous and cost-free process. Markets were mainly described as simple market exchanges where faceless buyers and sellers meet for an instant to exchange standardized goods at equilibrium prices. Secondly, energy exchanges are relatively new phenomenon. The justification of exchange trading became possible as a result of new institutional economics (NIE) and transaction cost theory (TCT) findings. Under conditions of positive transaction costs, incomplete foresight and bounded rationality – the conditions of the New Institutional Economics (NIE) – the institutional framework not only of firms but also of markets matters. Also, within this institutional framework the concept of “governance structure” was introduced. A high-performance system shall align transactions with governance structures in relation to their adaptive needs. Governance structures are properly regarded as part of the optimization problem. A shift from one structure to another may permit a simultaneous reduction in both the expense of writing a complex contract and the expense of executing it effectively in an adaptive, sequential way. The founders of NIE and TCT, having been investigating the stock and commodity exchanges, approached them as a measure of transaction costs for other-the-counter trades. However, they did not include exchange trading into classification of governance structures. As far as is known, it has not been described in this way in terms of NIE and TCT to date. Natural gas and electricity markets is a good examples of network industries, which are an appropriate case of institutional flexibility regarding the alignment between transactions and governance structures. “Liberalised” network industries needed and still need an “intense” design and re-design to be able to host any kind of markets and to interact with. Organized markets, energy exchanges have developed a required bridge between leaving long-term contracts and price promulgation. The hypothesis of energy exchange classification as a special type of governance structure, in the meaning of NIE and TCT, for network industries is discussed in this article.
Measuring scientific reasoning in kindergarten and elementary school: validating the Chinese version of the Science-K Inventory

Field: Psychology (Social Sciences)

Abstract Scientific reasoning is a twenty-first century skill that is important for economic growth and social prosperity. A growing body of research documents that basic scientific reasoning skills develop much earlier than initially assumed, with many young elementary school and even kindergarten-aged children showing emergent scientific reasoning skills. Many studies on early scientific reasoning have been conducted in Western countries, and there is a lack of validated instruments that can be used in cross-cultural work. The present paper reports on the findings of a study assessing the psychometric properties of the shortened Chinese version of the Science-K(indergarten) Inventory (SC-SKI). The SC-SKI consists of 10 items that assess children’s understanding of the nature of science, as well as their experimentation and data interpretation skills. Sixty-nine 6- to 7-year-olds from urban and rural schools in the Hunan province (China) participated in the study. The results showed an acceptable reliability of the SC-SKI (McDonald’s ω t = 0.60). The ability estimates obtained for children’s scientific reasoning (average performance was 47.5% correct) were comparable to those measured in German 6-year-olds (45.1% correct), and the urban sample outperformed the rural sample, supporting the ability of the SC-SKI to detect expected performance differences in young children’s scientific reasoning. A significant correlation between scientific reasoning and language skills ( r = 0.54, p < 0.05) confirms earlier findings and indicates construct validity. Taken together, the present study shows that the SC-SKI is a reliable and valid instrument that can be used to measure scientific reasoning in Chinese-speaking 6- to 7-year-olds.
Preparation, structure and magnetic study of a new linear 1-D Cu(II)–Gd(III) coordination polymer

Field: Chemistry (Physical Sciences)

A carboxylate-bridged Cu(II)–Gd(III) complex, [GdCu(CH2CH(CH3COO)4(H2O)4] n (NO3) n , was prepared and characterized. Single crystal X-ray analysis reveals the complex as a carboxylate-bridged 1-D Cu(II)–Gd(III) coordination polymer. The magnetic measurement showed this complex exhibiting weak ferromagnetic behavior.