jimnoneill/paper-to-field-training huggingface dataset:
Characterizing alternative splicing effects on protein interaction networks with LINDA

Field: Computer Science (Physical Sciences)

Abstract Motivation Alternative RNA splicing plays a crucial role in defining protein function. However, despite its relevance, there is a lack of tools that characterize effects of splicing on protein interaction networks in a mechanistic manner (i.e. presence or absence of protein–protein interactions due to RNA splicing). To fill this gap, we present Linear Integer programming for Network reconstruction using transcriptomics and Differential splicing data Analysis (LINDA) as a method that integrates resources of protein–protein and domain–domain interactions, transcription factor targets, and differential splicing/transcript analysis to infer splicing-dependent effects on cellular pathways and regulatory networks. Results We have applied LINDA to a panel of 54 shRNA depletion experiments in HepG2 and K562 cells from the ENCORE initiative. Through computational benchmarking, we could show that the integration of splicing effects with LINDA can identify pathway mechanisms contributing to known bioprocesses better than other state of the art methods, which do not account for splicing. Additionally, we have experimentally validated some of the predicted splicing effects that the depletion of HNRNPK in K562 cells has on signalling.
Effect of Processing Conditions on Microstructure: Al-Cu-Si Eutectic Alloy

Field: Materials Science (Physical Sciences)

Aluminium is widely used in various industries such as food, electrical and electronics, automotive, aerospace and construction due to its favorable properties such as malleability, corrosion resistance, environmental resistance and high strength-to-weight ratio. In aluminum-based casting alloys, the main alloying elements commonly used in industry are silicon, copper and magnesium. In this study, the microstructure properties of the Al-26.5Cu-6Si (wt.%) ternary eutectic alloy were examined in relation to directional solidification. The alloy was processed in a vacuum melting furnace and solidified directionally at various growth rates using a Bridgman type device. The experimental results revealed eutectic transformation of the Al-26.5Cu-6Si alloy, leading to the formation of matrix Al, lamella Al2Cu, and plate Si phases. Eutectic spacing was measured from the produced samples, and it was found that the values were significantly affected by the growth rate. The results of this study were compared to the experimental results of binary Al-Cu and ternary Al-Cu-Si-Fe eutectic alloys.
Elimination of Chloramphenicol in Rainbow Trout Receiving Medicated Feed

Field: Veterinary (Health Sciences)

Elimination of Chloramphenicol in Rainbow Trout Receiving Medicated Feed Chloramphenicol muscle residue levels in rainbow trout were determined after oral administration of 84 μg kg -1 d -1 of chloramphenicol for four days. Samples were taken one day before treatment and for 43 days after the treatment was over. Chloramphenicol was analysed using an in-house enzyme linked immunoassay (ELISA) validated against the criteria of the Commission Decision 2002/657/EC. Validation parameters confirmed that the method was appropriate for the detection of chloramphenicol at levels below the minimum required performance limit (MRPL) of 0.3 μg kg -1 . The highest chloramphenicol levels were observed on the first day after the treatment had ended (144.3 μg kg -1 ). Elimination was significant over the first seven days; significant differences were detected between days 1 and 3 (p<0.001), 3 and 5 (p<0.001), and 5 and 7 (p<0.05). Chloramphenicol levels dropped below MRPL to 0.17 μg kg -1 on day 9 after the end of treatment. From day 11 to 43, chloramphenicol residues were detectable in a range from 0.091 μg kg -1 (highest) to 0.011 μg kg -1 (lowest). Our results indicate that trout muscle tissue could be compliant with health requirements for consumption 10 days after withdrawal from chloramphenicol treatment.
Hybrid mechanism of electrical breakdown in ferroelectric materials under high-pressure shock loading

Field: Materials Science (Physical Sciences)

The unique ability of ferroelectrics to generate high voltage under shock loading is limited by electrical breakdown within the shock-compressed ferroelectric material. Breakdown is a hybrid process of initiation and growth. The possible mechanisms of electrical breakdown in ferroelectric films and bulk ceramics subjected to high-pressure shock loading are discussed and experiments designed to elucidate which mechanisms govern breakdown. Gigapascal shock loading experiments were performed on poled Pb0.99(Zr0.95Ti0.05)0.98Nb0.02O3 ferroelectric film specimens in the range of 32–156 μm thickness to determine the dependence of the breakdown field on thickness and on film specimens in the range of 4–16 mm length to determine the dependence of the breakdown field on the duration of shock compression. The resulting breakdown-field vs thickness and breakdown-field vs shock transit time dependencies are consistent with a hybrid electron emission initiation and Joule heating microchannel growth mechanism. Further analysis of data previously obtained on shock-compressed 0.27Pb(In1/2Nb1/2)O3–0.47Pb(Mg1/3Nb2/3)O3–0.26PbTiO3 ferrvoelectric single crystals and Pb(Zr0.65Ti0.35)O3, Pb0.99(Zr0.52Ti0.48)0.99Nb0.01O3, Pb0.99(Zr0.95Ti0.05)0.98Nb0.02O3 bulk ceramics is consistent with this dual mechanism. It appears that neither chemical composition nor microstructure (single crystal vs polycrystalline) of the ferroelectric material has a significant effect on the breakdown mechanism in shocked ferroelectrics.
Hydrogel Paper-Based Analytical Devices: Separation-Free In Situ Assay of Small-Molecule Targets in Whole Blood

Field: Chemical Engineering (Physical Sciences)

While colorimetric-based assays are very convenient to determine biomarkers in point-of-care testing (POCT), they often suffer from pretreatment procedures for separation of plasma or serum from whole blood samples. Here, we report a simple colorimetric paper-based analytical device (c-PAD) that is capable of performing sample-to-answer analysis by directly dropping the whole blood sample on paper. This is accomplished by utilizing sodium alginate hydrogel, which exhibits a nanometer-scale porous structure to effectively prevent the passage of large red blood cells and hemoglobin molecules, to encapsulate enzymes and chromogenic reagents. As the small targets in the blood sample enter the sensing region to trigger a chromogenic reaction, the resulting color signal is recorded by a smartphone. The interference from the red blood to the color signal can be completely avoided without the requirement of any separation process. The analytical performance of the method is evaluated by assaying glucose in real blood samples. The results show that rapid and accurate analysis can be achieved with the limit of detection as low as 0.12 mM. In addition, simultaneous detection of different targets (glucose, cholesterol, and triglycerides) in whole blood can be achieved by fabricating c-PAD with multiple sensing regions. Owing to its several essential advantages including an extremely simple procedure for fabrication, sample-to-answer analysis without tedious pretreatment, and capability to perform high-throughput analysis, the proposed c-PAD will be of great value in POCT applications of whole blood samples.
Using the Decision Case Method to Teach Legislative Policy Advocacy

Field: Social Sciences (Social Sciences)

Abstract Social work educators have long struggled with making policy practice real “more”, especially to micro-oriented students (Sundet & Kelly, 2002). The decision case method can generate excitement about social policy advocacy while educating students about current advocacy work, particularly if the case involves state or local efforts to influence policy. Such state/local cases make policy advocacy more accessible and engaging. Wanting to introduce our students to important efforts in our state to influence policy and encourage them to get involved, we wrote our own case, included in this article.
Movement Activists and Partisan Insurgents

Field: Social Sciences (Social Sciences)

On the opening day of the 1972 Democratic convention, the women's caucus gave George McGovern a standing ovation. Its first meeting was packed, with 700 female delegates in attendance, exuberant over their numbers at the convention—triple the representation from four years earlier—and their new clout in presidential politics. Of all of the presidential candidates appearing, only Shirley Chisholm, the first African-American woman to run for president, was greeted with enthusiasm comparable to the warm reception for McGovern. Most of the women at the meeting were fervently anti-war and respected McGovern for his early and courageous stance on Vietnam. However, the size of the gathering attested to another of McGovern's achievements: his chairing of the reform commission that had rewritten the Democratic Party's rules on delegate selection, leading to the huge leap in the representation of women. As Liz Carpenter, a former White House aide to LBJ, put it when introducing McGovern, “We know we wouldn't be here if it hadn't been for you.”
Transplacental Passage of the Metalloporphyrin and Prenatal Suppression of Hyperbilirubinemia in the Newborn Animal

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Sn(tin)-protoporphyrin, a potent competitive inhibitor of heme oxygenase, can suppress hyperbilirubinemia in animal neonates and significantly reduce plasma bilirubin levels in animals and man. To further explore the biological actions and metabolic disposition ofSn-protoporphyrin, we have examined its effect in the suckling neonate when administered to the mother either 24-48 h before or immediately after birth. Sn-protoporphyrin, when administered before birth, crossed the placental membranes, inhibited fetal heme oxygenase, and suppressed the transient hyperbilirubinemia that occurs in the neonate after birth in a dose-dependent manner. Tissue heme oxygenase activity in the neonate was also lowered in a dose-dependent manner. The blood-brain barrier of the neonate was permeable to Sn-protoporphyrin for a period of between 20-28 d of postnatal life. Snprotoporphyrin, however, was not retained in brain, but left the brain space with a t1/2 of 1.7 d. In addition, Sn-protoporphyrin administered once at birth to neonates inhibited brain heme oxygenase in a dose-dependent manner. The results of this study demonstrate that Sn-protoporphyrin can cross the placental membranes, inhibit tissue heme oxygenase activity in the fetus, and can also, following such prenatal treatment, suppress the hyperbilirubinemia of the newborn animal.
The Impact of Disorder–Order Switching on Protein Sequence Evolution

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

Protein structure is a major determinant of protein evolution at the residue level. It is especially challenging to elucidate the relationship between structure and evolution for proteins that adopt several different conformations due to their function. Previously, we showed that proteins that switch between different native states are on average under stronger selective pressure than proteins with a single native state. Here, we analyzed evolutionary rates at the residue level for proteins that switch between disordered and ordered states in the yeast proteome. We show that while proteins with completely disordered regions generally evolve more rapidly than structured proteins, proteins with disorder-order switching regions evolve significantly more slowly on average. Surprisingly, proteins with disorder-order switching regions on average evolve even more slowly than conformational switches, which are known to be highly conserved. The elevated selective pressure on proteins with disorder-order switching regions is exerted on the entire protein, such that even the ordered residues in these proteins are on average more conserved than the ordered residues in structured proteins. While disordered residues generally evolve more rapidly than ordered residues within a protein, disordered regions that can switch into ordered states are highly conserved compared with other disordered residues. Overall, our results suggest that the necessity to encode and maintain coupled folding and binding imposes a unique and strong selective pressure on the entire protein.
Outcomes following Semicircular Canal Plugging

Field: Medicine (Health Sciences)

Objectives: 1) Examine audiometric outcomes following semicircular canal plugging for either superior semicircular canal dehiscence syndrome or refractory positional vertigo. 2) Review symptom control rates and complication rates for canal plugging procedures. Methods: Retrospective chart review at a private neurotologic tertiary referral center. Patients undergoing semicircular canal plugging for superior semicircular canal dehiscence syndrome or refractory positional vertigo from January 1, 2007, to December 31, 2012, were included. Pre‐ and postoperative audiometry, operative findings, and clinical symptoms were assessed through chart review. Acoustic reflex testing, vestibular testing, and canal dehiscence size were examined in superior canal dehiscence patients. Results: A total of 28 patients underwent a canal plugging procedure during the study period: 24 superior canal dehiscence syndrome patients and 4 posterior canal occlusion patients. Postoperative air conduction pure‐tone averages were 22.5 and 13.0 dB for these two groups, respectively, compared to their preoperative values of 21.1 and 11.0 dB. The average pre‐ and postoperative word‐recognition scores for the entire cohort were 96.2% and 94.0%. Vestibular evoked myogenic potential data showed reduced thresholds in 7 canal dehiscence patients. The average size of the canal dehiscence, based on preoperative radiological measurements, was 3.4 mm. Surgical complications were limited to one temporary facial weakness (Grade 2). Complete symptom improvement was noted in 35.7% of all patients, while 16.7% of canal dehiscence patients reported no change in symptoms. Conclusions: Semicircular canal plugging procedures are associated with excellent hearing outcomes and may reduce preoperative symptoms in patients with canal dehiscence and refractory positional vertigo.
Résultats perturbatifs dans les théories de supergravité quantique par la théorie des cordes

Field: Physics and Astronomy (Physical Sciences)

Les théories de supergravité sont des extensions supersymmetriques de la relativité générale (RG) d'Einstein. Leur comportement ultraviolet (UV) est meilleur que celui de la RG car les contributions bosoniques et fermioniques se compensent dans les diagrammes en boucles. La supergravité maximale a le meilleur comportement UV, toutefois les prédictions les plus précises venant aussi bien de la théorie des champs que de la théorie des cordes indiquent que la théorie devrait elle aussi souffrir de divergences UV, à partir de 7 boucles. Cette question ouverte constitue un cadre dans lequel peut être problématisés ma thèse. En général, l'approche que j'ai suivie consiste à étudier les amplitudes de diffusion en théorie des cordes dans la limite ou la longueur de la corde devient nulle; on s'attend ainsi à retrouver les amplitudes de diffusion de supergravité. Curieusement, on sait très peu de choses sur cette limite au délà d'une boucle. Une part importante de mon travail thèse a consisté à développer des outils mathématiques basés sur la géométrie tropicale pour décrire cette limite en genre deux et au délà. Afin de tester la précision des prédiction de la théorie des cordes, dans ma thèse j'ai aussi travaillé sur le comportement UV des théories de supergravité demi-maximale. Nous avons montré un théorème de non-renormalisation qui expliqué l'absence de divgerence à 3 boucles et en prédit une à 4 boucles. Enfin je me suis intéressé aux techniques utilisées en théorie des champs pour calculer ces amplitudes à haut nombre de boucles en théorie des champs, et notament à la "double copie BCJ", dont avons proposé la première analyse à une boucle depuis la théorie des cordes.
Intrinsic Motivation of University Students in Participating in Physical Fitness Training Programs

Field: Psychology (Social Sciences)

LANGUAGE NOTE | Document text in English; abstract also in Chinese.The purpose of this study was to examine the intrinsic motivation of University students in pursuing physical fitness training programs. 224 university undergraduate students (81 males and 143 females) who participated voluntarily in fitness training courses were included in this study. Participants were asked to complete a 7-item questionnaire to find out their intrinsic motivation of participating in the fitness training programs. Ratings of the questionnaire range from 1 (strongly disagree) to 5 (strongly agree). The motivation factors were ranked according to their mean scores. It was found that "to keep fit and strong" was top of the list, followed by "to improve health" and "to improve outlook". The implications of the rank order were discussed in the paper. Factor analysis of the motivation factors showed that there were two sub-factor components: physical factor and social factor. The reliability coefficients of the factors were 0.58 and 0.83 respectively. One way ANOVA results showed that significant difference was only found between genders in relation to the social factor. Social factor was seen to be a more important motivating factor in female participants of physical fitness training programs.本文旨在研究大學生參加健身訓練課程的內發動機。共有二百二十四名大學本科生自願參加這個研究，他們在參加課程後填寫一份有七條題目的問卷。問卷答案幅度由一(強烈反對)至五(強烈贊成)。動機因素方面以平均值去排列等級。結果顯示"保持身體強健"居於首位，跟著的是"改善健康"和"改善外表"。文中亦提及排列等級結果的含意。因子分析結果指出問卷內容有兩個次組合："體質"和"社交"。它們的信度係數分別是0.58和0.83。單向方差分析法表示"性別"和"社交"有顯著差異。"社交"被認為是女性參加健身訓練課程的一個重要內發動機。
Russian federation

Field: Economics, Econometrics and Finance (Social Sciences)

In 2013, the value of merchandise exports of the Russian Federation increased slightly by 0.5 percent to reach 527.3 bln US$, while its merchandise imports decreased slightly by 0.4 percent to reach 314.9 bln US$ (see graph 1, table 2 and table 3). The merchandise trade balance recorded a moderate surplus of 212.3 bln US$ (see graph 1). The largest merchandise trade balance was with MDG Developed Europe at 109.4 bln US$ (see graph 4). Merchandise exports in the Russian Federation were diversified amongst partners; imports were also diversified. The top 21 partners accounted for 80 percent or more of exports and 21 partners accounted for 80 percent or more of imports (see graph 5). In 2013, the value of exports of services of the Russian Federation increased substantially by 13.0 percent, reaching 66.0 bln US$, while its imports of services increased substantially by 17.9 percent and reached 126.4 bln US$ (see graph 2). There was a large trade in services deficit of 60.4 bln US$.
“Zeroes,” “ridges,” and poles, in the scattering amplitudes of elastic waves echoing from resonating fluid spheres in solids and liquids

Field: Physics and Astronomy (Physical Sciences)

We study the “resonance parts” of the scattering amplitudes of compressional or shear waves, returned when compressional or shear waves are incident on fluid spheres contained in either solids or in dissimilar fluids. The resonance parts are obtained after suitable smooth backgrounds are subtracted from each composite partial-wave amplitude. The starting point of the analysis is the three-dimensional graph of any of the modular surfaces |a−1fnPP|, |a−1fnPS|, |a−1fnSP|, and |a−1fnSS| plotted versus mode order n, and nondimensional frequency ka. We found simple expressions for the (not necessarily straight) lines of zeros that constitute the boundaries or demarcation lines of each of the “ridges” that appear so evidently in the plots. These “ridges,” which are inclined with respect to the n and ka axes, exhibit marked cleavages, and the “peaks” present in them (i.e., the resonances) are spaced in a peculiar way that is, (a) predictable from the analysis, and (b) that yields information about the material composition of the scatterer. The analytic expressions for the lines connecting the tips of the peaks along a given ridge has also been determined. Each “ridge” is shown to be associated with a “creeping wave” and it is the graphic visualization of the elastic analog of a “Regge pole.” [H. Überall is also at Catholic University, Washington, DC, and was additionally supported by Code 421 of ONR.]
On the issue of the shedding of cannabis seeds

Field: Agricultural and Biological Sciences (Life Sciences)

The task of our research was to determine the retention strength of cannabis seeds in the inflorescence of a low-yielding dioecious variety YUS-9 and a monoecious variety Diana prone to shedding, and in this regard, to study the anatomical and morphological features of the structure of their bracts and morphological features of the structure of their bracts and the area of attachment of seeds to the peduncle. Based on the conducted studies, it was revealed that the larger the area of attachment of seeds to the peduncle and the more developed the bracts, the higher the retention strength of hemp seeds in the inflorescence. When selecting cannabis for resistance to shedding, it is necessary to take into account the anatomical and morphological features of the structure of the bracts and the size of the area of attachment of seeds to the peduncle. The developed technique makes it possible to characterize the variety or the initial breeding material by the strength of the retention of seeds in the inflorescence.
Tick‐induced allergies: mammalian meat allergy and tick anaphylaxis

Field: Medicine (Health Sciences)

Mammalian meat allergy after tick bites and tick anaphylaxis are the most serious tick-induced allergies. They are often severe, should be largely avoidable and offer fascinating insights into the development and prevention of allergies. Australian clinicians reported the first cases of tick anaphylaxis and discovered the association between tick bites and the development of mammalian meat allergy. The subsequent finding of the allergen epitope within the meat responsible for the allergic reaction, α-gal (galactose-α-1,3-galactose), stimulated further interest in this emergent allergy. Reports of mammalian meat allergy associated with bites from several tick species have now come from every continent where humans are bitten by ticks. The number of diagnosed patients has continued to rise. Clinically, mammalian meat allergy and tick anaphylaxis present quite differently. The prominent role of cofactors in triggering episodes of mammalian meat allergy can make its diagnosis difficult. Management of mammalian meat allergy is complicated by the manifold potential therapeutic implications due to the widespread distribution of the mammalian meat allergen, α-gal. Exposures to α-gal-containing medications have proved lethal in a minority of people, and fatal tick anaphylaxis has been reported in Australia. Prevention of tick bites is prudent and practicable; killing the tick in situ is crucial to both primary and secondary prevention of allergic reactions. Mechanisms in the development of mammalian meat allergy constitute a paradigm for how allergies might arise.