jimnoneill/paper-to-field-training huggingface dataset:
Research Methods: The Cross-Cultural Method

Field: Social Sciences (Social Sciences)

A GOOD method, to paraphrase Guthrie, is at best a tool by which explanation is furthered. In the final analysis a theory or method stands or falls upon its utility. The cross-cultural method presents a number of paradoxes which the reader must keep in mind as he considers it as a possible tool for research. First, altho the method has been in existence for some 70 years, not until recently has either its scope or its usefulness been recognized. Second, unlike many areas of research, there are relatively few studies which have been published utilizing this particular method. An evaluation of a methodology usually is based upon a large amount of published research which the reviewer can refer to and evaluate. Such is not the case with this particular method. However, despite the paucity of published research this particular method has had a great effect upon behavioral science, and in relation to recent work may have shown itself to be the most sensitive methodology available for those who wish to accomplish interdisciplinary research in the behavioral sciences. Since this is the first article dealing with the method in the REVIEW, some recapitulation of its history is appropriate. This is particularly true since the cross-cultural method is often confused with another valuable approach to the study of behavior, namely, the comparative or culture-personality study.
Compact surface wave polarization splitter based on the metallic-dielectric-air waveguide

Field: Engineering (Physical Sciences)

We proposed a compact surface wave polarization splitter based on the metallic-dielectric-air (MDA) waveguide with an slit surrounded by asymmetric corrugations. The incident light coupled to the MDA waveguide through the aperture is split into TE- and TM-polarized electromagnetic surface modes by the polarization-sensitive corrugations on each side. Polarization extinction ratios better than 20 dB are achieved for both polarizations. The structure would be interesting for a variety of optical devices and nanophotonics.
Expression of S100A6 in Rat Hippocampus after Traumatic Brain Injury Due to Lateral Head Acceleration

Field: Neuroscience (Life Sciences)

In a rat model of traumatic brain injury (TBI), we investigated changes in cognitive function and S100A6 expression in the hippocampus. TBI-associated changes in this protein have not previously been reported. Rat S100A6 was studied via immunohistochemical staining, Western blot, and reverse transcription-polymerase chain reaction (RT-PCR) after either lateral head acceleration or sham. Reduced levels of S100A6 protein and mRNA were observed 1 h after TBI, followed by gradual increases over 6, 12, 24, and 72 h, and then a return to sham level at 14 day. Morris water maze (MWM) test was used to evaluate animal spatial cognition. TBI- and sham-rats showed an apparent learning curve, expressed as escape latency. Although TBI-rats displayed a relatively poorer cognitive ability than sham-rats, the disparity was not significant early post-injury. Marked cognitive deficits in TBI-rats were observed at 72 h post-injury compared with sham animals. TBI-rats showed decreased times in platform crossing in the daily MWM test; the performance at 72 h post-injury was the worst. In conclusion, a reduction in S100A6 may be one of the early events that lead to secondary cognitive decline after TBI, and its subsequent elevation is tightly linked with cognitive improvement. S100A6 may play important roles in neuronal degeneration and regeneration in TBI.
Mutations at embB Codon 306 Are an Important Molecular Indicator of Ethambutol Resistance in Mycobacterium tuberculosis

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

ABSTRACT Ethambutol resistance in clinical Mycobacterium tuberculosis isolates is associated primarily with missense mutations in the embB gene. However, recent reports have described the presence of embB mutations, especially those at embB codon 306, in isolates susceptible to ethambutol. To clarify the role of embB mutations in ethambutol resistance, we sequenced the ethambutol resistance-determining region in spontaneous ethambutol-resistant mutants. In our study, 66% of spontaneous mutants contained a single point mutation in embB , with 55% of these occurring at embB 306. The MIC of ethambutol for spontaneous mutants was increased two- to eightfold relative to the pansusceptible M. tuberculosis strains from which the mutants were generated. To further characterize the role of embB 306 mutations, we directly introduced mutant alleles, embB ( M306V ) or embB ( M306I ), into pansusceptible M. tuberculosis strains and conversely reverted mutant alleles in spontaneous ethambutol-resistant mutants back to those of the wild type via allelic exchange using specialized linkage transduction. We determined that the MIC of ethambutol was reduced fourfold for three of the four spontaneous ethambutol-resistant embB 306 mutants when the mutant allele was replaced with the wild-type embB allele. The MIC for one of the spontaneous mutants genetically reverted to wild-type embB was reduced by only twofold. When the wild-type embB allele was converted to the mutant allele embB ( M306V ), the ethambutol MIC was increased fourfold, and when the allele was changed to M306I, the ethambutol MIC increased twofold. Our data indicate that embB 306 mutations are sufficient to confer ethambutol resistance, and detection of these mutations should be considered in the development of rapid molecular tests.
Mechanisms, diagnosis and management of eosinophilic asthma

Field: Medicine (Health Sciences)

Asthma is a common chronic airway disease affecting about 334 million people worldwide, and up to 10% of asthma patients have severe asthma, which may be uncontrolled despite high doses of the standard treatment modifiers and may require the use of chronic oral corticosteroids. It is the most common chronic disease in children in the developed countries. Asthmamanifests as reversible airflow obstruction, due to airway inflammation, bronchial smooth muscle contraction, increased mucus secretion, vascular engorgement, mucosal oedema, and airway hyper responsiveness, which leads to airflow obstruction and symptoms of asthma. Eosinophilic asthma is a phenotype of asthma that is usually very severe and persistent, with frequent exacerbations. It is usually observed in adult asthmatic patients, although it may occur in children. It is characterized by the presence of high levels of eosinophils, and CD+4 Th2 cells in the lungs and airways, which can be demonstrated by a raised eosinophil count in blood, and induced sputum or bronchial biopsy. It is managed in a similar stepwise treatment for childhood-onset asthma, but some of the patients with eosinophilic asthma do not respond to this standard treatment including inhaled or oral corticosteroids. The logical approach to treat corticosteroid-refractory asthma is to target the eosinophilic interleukins which cause airway inflammation using monoclonal antibodies to block their activity on the eosinophils, and Th2 cells. Currently, the following monoclonal antibodies are used in the treatment of eosinophilic asthma: IgE antibody such as omalizumab, or interleukin receptor 5, or 4, and 13 antagonists, such mepolizumab, reslizumab, and dupilumab. These novel agents have proved to be very useful in relieving the symptoms, and in improving the forced expired volume in one second (FEV1), and in reducing exacerbations. They are also steroid-sparing agents, and improve the quality of lifein this debilitating phenotype of asthma.
Unique hue data for colour appearance models. Part III: Comparison with NCS unique hues

Field: Chemistry (Physical Sciences)

Abstract In this study, Swedish Natural Color System (NCS) unique hue data were used to evaluate the performance of unique hue predictions by the CIECAM02 colour appearance model. The colour appearance of 108 NCS unique hue stimuli was predicted using CIECAM02, and their distributions were represented in a CIECAM02 a c – b c chromatic diagram. The best‐fitting line for each of the four unique hues was found using orthogonal distance regression in the a c – b c chromatic diagram. Comparison of these predicted unique hue lines (based on the NCS data) with the default unique hue loci in CIECAM02 showed that there were significant differences in both unique yellow (UY) and unique blue (UB). The same tendency was found for hue uniformity: hue uniformity is worse for UY and UB stimuli in comparison with unique red (UR) and unique green (UG). A comparison between NCS unique hue stimuli and another set of unique hue stimuli (obtained on a calibrated cathode ray tube) was conducted in CIECAM02 to investigate possible media differences that might affect unique hue predictions. Data for UY and UB are in very good agreement; largest deviations were found for UR. © 2014 Wiley Periodicals, Inc. Col Res Appl, 40, 256–263, 2015
Employing deep mutational scanning in the Escherichia coli periplasm to decode the thermodynamic landscape for amyloid formation

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

Deep mutational scanning (DMS) assays provide a powerful method to generate large-scale datasets essential for advancing AI-driven predictions in biology. The tripartite β-lactamase assay (TPBLA), in which a protein of interest is inserted between two domains of β-lactamase, has previously been reported as capable of detecting and quantitating the aggregation of proteins and biologics in the oxidizing periplasm of Escherichia coli and used as a platform for identifying small molecule inhibitors of aggregation. Here, we repurpose the TPBLA into a high-throughput DMS platform. We validate this format using a single-site saturation library of the intrinsically disordered peptide Aβ 42 , linked to Alzheimer’s disease, demonstrating strong agreement between observed variant fitness scores and variant behavior using our previously reported low-throughput TPBLA. The results of DMS revealed variant fitness scores that correlate with known amyloid-promoting regions. An in silico approach using FoldX-derived per-residue thermodynamic stability confirmed that the TPBLA reports on amyloid fibril stability. In vitro experiments support this finding, showing a strong correlation between variant fitness scores and the critical concentration of amyloid formation. Machine learning using the DMS dataset identified β‐sheet propensity and polarity as primary drivers of variant fitness scores. The derived model is also able to predict thermodynamically stabilizing regions in other amyloid systems, underscoring its generalizability. Collectively, our results demonstrate the TPBLA as a versatile platform for generating robust datasets to advance predictive modeling and to inform the design of aggregation‐resistant proteins.
Infrared and resonance Raman spectroscopic studies of 1‐hydroxy‐9,10‐anthraquinone and its metal complexes

Field: Chemistry (Physical Sciences)

Abstract Infrared and resonance Raman spectra of 1‐hydroxy‐9, 10‐anthraquinone, its deuteriated and deprotonated forms and its metal chelates with Cu II , Ni II and Co II ions are presented. Vibrational assignments of the carbonyl, hydroxyl and the chelating unit of this chromophore are emphasized. It is found that the different metal ions force delocalization of the electrons on the chelate rings to different extents. The intensities of the Raman bands under resonance conditions suggest that the electronic band in the visible region is mainly of a charge‐transfer type from the metal to the ligand.
Material Properties of High-strength High Chromium TWIP Steel with Increased Corrosion Resistance

Field: Materials Science (Physical Sciences)

Twinning induced plasticity (TWIP) steels are a class of high-strength steels that have been devel-oped for their outstanding ductility and strength properties. TWIP refers to the fact that these steels display an unusually high degree of deformation before fracture due to the formation of twins during deformation. TWIP steels could be used in a variety of industries for structural applications or com-ponents that need to withstand high levels of stress and deformation. This article deals with the de-velopment of high strength with fully austenitic microstructure and high chromium content. Micro-structure, mechanichal and corrosion properties of this steel were studied.
Machine Learning Enabled Prediction of Solvent-Based Reaction Energetics

Field: Computer Science (Physical Sciences)

Despite recent advancements in molecular dynamics (MD) methods, the computational costs of \\emph{ab initio} molecular dynamics simulations for explicit solvation systems are still too significant. If accuracy is to be left uncompromised, new methods must be employed to reduce computational expenses. This work focuses on the development of machine learning (ML) models as proxy models for Car-Parrinello molecular dynamics (CPMD) metadynamics simulations in condensed-phase biomass reactions. Explicit solvation CPMD metadynamics simulation data of HMF undergoing protonation in a solution of dimethyl sulphoxide (DMSO) and water is used to train various model architectures to make time-series predictions of their probability distribution functions (PDFs). For each model architecture, three models were trained to fully predict the system, one for each of the following species: reactants, water and DMSO. Each model was tested assuming an initial simulation had been performed and the proxy models were used to complete the simulation. The long short-term memory (LSTM) autoencoder and 3D convolutional neural networks (CNN)-LSTM autoencoder architectures failed to accurately capture PDF magnitudes and locations. A binary relevance 3D CNN-LSTM autoencoder, employing different loss functions, showed marginal improvement but struggled to predict probability locations over a large horizon. Models trained on principal component analysis (PCA)-transformed and dynamic PCA (DPCA)-transformed data showed promise in training but failed in testing. Models trained on PDFs without "dead voxels" (zero probability voxels independent of time) and atomic Cartesian coordinates perform well during training but encounter challenges in testing due to teacher forcing. Teacher forcing is a training method that can potentially make the trained model over-reliant on ground truth, which is unavailable if the model is to be used as a proxy. Despite attempts to mitigate teacher forcing effects through scheduled sampling, no model architecture achieves reliable long-term predictions without ground truth data. However, the model trained on Cartesian coordinates demonstrated proficiency in making short-term predictions regarding the atomic configuration of the system.
Breeding of the holstein horse on the stud-farm in College of agriculture in Križevci

Field: Agricultural and Biological Sciences (Life Sciences)

Organizirani uzgoj holstein pasmine konja poceo je 1980 godine u tadasnjem Poljoprivrednom institu u Križevcima (sadasnji naziv Visoko gospodarsko uciliste u Križevcima). Prva grla su uvežena 8. ožujka 1980 godine, a to su bile cetiri bređe kobile iz tri razlicite uzgojne linije. Godine 1981. uvežene su jos dvije kobile i pastuh. U periodu od 1980. do 2005. u rasplodu je bilo 32 kobile i 20 pastuha. Tijekom ovog perioda ukupno je oždrijebljeno 131 živo ždrijebe, a od toga su bila muska 77 (58.78 %), a ženska 54 (41.22 %) ploda. U periodu od 25 godina je bilo 15 pobacaja od cega je u 4 slucaja bilo rijec o blizancima, a u jednom trojke. Najveci broj potomaka potjece od pastuha Fridericusa, Calypsa i Amadeusa, a najvise ždrebadi oždrijebile su kobile Mollina i Nordmoeve. Prosjecna dužina trajanja graviditata je 333 dana.
Public Perception of the Vegetative State/Unresponsive Wakefulness Syndrome: A Crowdsourced Study

Field: Medicine (Health Sciences)

Background: The vegetative state (VS)/unresponsive wakefulness syndrome (UWS) denotes brain-injured, awake patients who are seemingly without awareness. Still, up to 15% of these patients show signs of covert consciousness when examined by functional magnetic resonance imaging (fMRI) or EEG, which is known as cognitive motor dissociation (CMD). Most experts prefer the term unresponsive wakefulness syndrome to avoid the negative connotations associated with vegetative state and to highlight the possibility for CMD. However, the perception of VS/UWS by the public has never been studied systematically. Methods: Using an online crowdsourcing platform, we recruited 1297 participants from 32 countries. We investigated if vegetative state and unresponsive wakefulness syndrome might have a different influence on attitudes towards VS/UWS and CMD. Results: Participants randomized to be inquired about the vegetative state believed that CMD was less common (mean estimated frequency in unresponsive patients 38.07% &plusmn; SD 25.15) than participants randomized to unresponsive wakefulness syndrome (42.29% &plusmn; SD 26.63; p=0.016). Attitudes towards treatment withdrawal were similar. Most participants preferred unresponsive wakefulness syndrome (60.05%), although a sizeable minority favored vegetative state (24.21%; difference 35.84%, 95% CI 29.36&nbsp;to&nbsp;41.87; p&lt;0.0001). Searches on PubMed and Google Trends revealed that unresponsive wakefulness syndrome is increasingly used by academics but not lay people.Discussion: Simply replacing vegetative state with unresponsive wakefulness syndrome may not be fully appropriate given that 1 of 4 prefer the first term. We suggest that physicians take advantage of the controversy around the terminology to explain relatives the concept of CMD and its ethical implications.
REsolution of Symptoms afTer Oesophago-gastric cancer REsection delphi (RESTOREd)—standardizing the definition, investigation and management of gastrointestinal symptoms and conditions after surgery

Field: Medicine (Health Sciences)

Abstract Background Oesophago-gastric cancer surgery negatively affects quality of life with a high postoperative symptom burden. Several conditions that may be diagnosed and treated after surgery are recognised. However, consensus regarding their definition and management is lacking. This study aimed to develop consensus regarding the definition, investigation and management of the common symptoms and conditions, and triggers to consider disease recurrence, as a foundation for improving management and quality of life in these patients. Method Modified two-round Delphi consensus study of a multidisciplinary expert panel. Results Eighty-six of 127 (67.7%) and 77 of 93 (82.8%) responses were received in rounds 1 and 2. Consensus was achieved in defining 26 symptoms. For 10 conditions (anastomotic stricture, acid reflux, non-acid reflux, biliary gastritis, delayed gastric emptying, dumping syndrome, exocrine pancreatic insufficiency, bile acid diarrhoea, small intestinal bacterial overgrowth and carbohydrate malabsorption), definitions, diagnostic criteria, first- and second-line investigation and first-line treatments were agreed. Consensus was not reached for third-line investigation of some conditions, or for second-, third- or fourth-line treatments for others. Twelve of 14 (85.7%) symptoms were agreed as triggers to consider cancer recurrence, during the early (&lt;1 year) and late (&gt;1 year) postoperative periods. Conclusion Expert consensus regarding symptoms, conditions and triggers to consider investigation for recurrence after oesophago-gastric cancer surgery was achieved. This may allow standardization and timely diagnosis and treatment of postoperative conditions, reducing variation in care and optimizing patients’ quality of life.
EMA, endoscopic, ultrasound and acoustic study of two secondary articulations in Moroccan Arabic: Labial-velarisation vs. emphasis

Field: Arts and Humanities (Social Sciences)

Based on three physiological experiments (electromagnetic articulography, endoscopy and ultrasound) carried out separately with two speakers, but with one subject in common, we demonstrate that the back articulation of the Moroccan Arabic emphatic stop consonants can be considered as pharyngealised, i.e. produced with a constriction in the oro-pharyngeal cavity. The emphatics /t d/1 are not velarised, and /d/ has a slight degree of labialisation. MA geminate labials, generally considered as ‘labialised’, are clearly velarised in accord with phonological analyses by Heath (1987) and Elmedlaoui (1995), and not emphatic or pharyngealised as was predicted by Mitchell (1993). These labials are labial-velarised consonants since they are also slightly more labialised compared to their singleton cognates. We confirm that the labialisation observed in word initial clusters /#C1C2/, where /C1/ or /C2/ is a velar or uvular consonant, is associated with /C1/ even when this latter is coronal. Labialised dorsals (velars and uvulars: /kw, ɡw, qw, χw, ʁw/) are not only labialised, but also more retracted than their non-labialised counterparts.
GUT-scale inflation with sizeable tensor modes

Field: Physics and Astronomy (Physical Sciences)

A sizeable tensor-to-scalar ratio, such as recently claimed by BICEP2, would\nimply a scale of inflation at the typical scale of supersymmetric grand\nunification. This could be an accident, or strong support for supersymmetric\ntheories. Models of F-term hybrid inflation naturally connect the GUT scale\nwith the inflationary scale, but they also predict the tensor-to-scalar ratio\nto be unmeasurably small. In this work we analyze a general UV embedding of\nF-term hybrid inflation into a supergravity theory with a general Kahler\npotential. The CMB observables are generated during the early phase of\ninflation, at large inflaton values, where the potential is dominated by\nPlanck-suppressed operators. Tuning the leading higher-order terms can give an\ninflaton potential with sizeable tensor fluctuations and a field excursion\nwhich is still sub-Planckian but close to the Planck scale, as expected from\nthe Lyth bound.\n
Characterize the role of cancer associated fibroblast (CAFs) derived IL-32 in esophageal squamous cell carcinoma (ESCC)

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

Abstract Cancer-associated fibroblasts (CAFs) are localized adjacently to cancer cells at all stages of esophageal squamous cell carcinoma (ESCC) progression, and their functional contributions to this process are emerging. Our previous studies have identified FGFR2 as CAFs specific marker in ESCC. In this study, using microarray analysis, we identified IL-32 was the most differentially expressed cytokine in CAFs in patients with ESCC. Flow cytometric analysis and western blot have revealed markedly increased IL-32 in FGFR2+ CAFs from ESCC tumor specimens, compared with non-tumor epithelial tissues. IL-32 treatment could promote prosurvival effect in tumor cell from upon cisplatin or 5-Fu mediated apoptosis in culture and human ESCC tumor-bearing nude mice. In contrast, knockdown of IL-32 expression in CAFs by shRNA reduce tumor cell viability in reconstituted mouse model upon cisplatin or 5-Fu treatment. Mechanistic study shows that IL-32 treatment significantly downregulated caspase 3/9 and upregulated Bcl-2 expression by ESCC tumor upon Cisplatin or 5-Fu stimulation. In contrast, blockage of type II IFN signaling in CAFs resulted in significantly reduced IL-32 secretion and increased apoptotic cell death of ESCC. Together, these findings have suggested a critical role of CAFs derived IL-32 in prosurvival effect ESCC and thereby exacerbating cancer development, which suggested that IL-32 blockade may serve as potential therapeutic target for ESCC.