jimnoneill/paper-to-field-training huggingface dataset:
Molecular Mechanisms of Alternative Splicing Regulation: An Investigation of the Spliceosome Repressed by Hnrnp L on Cd45 Exon 4

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

Alternative splicing is a key step in gene regulation and involves the differential selection of splice sites to generate different pre-mRNA transcripts. It has been shown that 90-95% of pre-mRNAs are alternatively spliced in human cells. Pre-mRNA splicing is catalyzed the spliceosome, which consists mainly of the U1, U2, U4, U5 and U6 snRNP, and about a hundred of non-snRNP proteins. Splicing regulators that bind to enhancer or silencer elements on the pre-mRNA can alter assembly of these spliceosome components. Understanding how splicing regulators control spliceosome assembly will bring insights to the prediction of splice site choices. In our lab, we used CD45 as a model gene for studying alternative splicing and spliceosome assembly. The exonic silencer sequence (ESS1) within CD45 exon 4 is bound by hnRNP L to induce its skipping. HnRNP L represses spliceosome assembly at a step after the binding of U1 and U2 snRNP on either side of the exon. My goal is to understand how hnRNP L perturbs U1 snRNP binding at the 5' splice site (5' ss) to cause the skipping of CD45 exon 4.\nUsing psoralen- and UV-crosslinking analysis, U1 snRNP and other protein components that associate with the sequences around the 5' ss within the hnRNP L-repressed spliceosome complexes were compared with the control complexes. These studies revealed that hnRNP L recruits hnRNP A1 to the 3' end of exon 4 to induce an extended pairing interaction between the U1 snRNA and the 5' ss. Splicing assays in vitro and in cells further demonstrated that hnRNP A1 and the U1 snRNA binding at the 3'end of exon 4 are required for hnRNP L-mediated skipping of exon 4. Further analysis of other exons repressed by hnRNP L or A1 suggests the potential for the extended U1 pairing interactions with these exons. These data imply that induction of U1 interactions with the exonic region nearby a 5' ss could be a widespread mechanism in inducing the skipping of exon. To further determine how the extended U1 binding affects the subsequent spliceosome assembly steps, hnRNP L-repressed spliceosome complexes were purified. This analysis revealed that association of U6 snRNP with the 5'ss, and recruitment of NTC components, are blocked in the hnRNP L-repressed complexes. Moreover, enhancing binding of U6 to the 5'ss overcomes the effect of the extended U1 interaction, thereby increasing the splicing of the hnRNP L-repressed substrate. These results provide the first example showing that the U1/U6 switch, a structural rearrangement during the catalytic activation of the spliceosome, is a naturally occurring point for regulating alternative splicing. This study also suggests that splicing regulators that alter U1 binding, or spliceosome components that associate with the 5' ss after U1 binding, are important factors for determining the usage of the 5'ss.
Exploratory eye movements and visual Hemi-Neglect

Field: Neuroscience (Life Sciences)

The severity of visual hemineglect (VHN), as defined by a VHN Index from scores obtained on letter cancellation and visual matching tests, was compared to eye movement behavior during a visual searching task in a group of right-hemisphere stroke patients and a group of age-matched normal controls. A strong negative correlation was obtained between the VHN Index and eye movement Exploration Time of the left visuospatial field for the stroke patients, but not for the control subjects. Further analyses failed to discriminate Exploration Time performance of stroke patients with mild VHN from the performance of control subjects, but did discriminate stroke patients with marked VHN from each of these two groups. Covarying for the presence of a left-visual-field sensory defect slightly reduced the significance level of this finding. The results and questions raised by this study are discussed in the context of developing an operational definition for VHN using the method of directly monitoring eye movement.
Molecular identification of Cryptosporidium baileyi in Muscovy ducks (Cairina moschata domesticus) in free-range production systems

Field: Veterinary (Health Sciences)

ABSTRACT: Cryptosporidiosis is considered an infection with impact on animal health. It has been associated with high morbidity and mortality rates, leading to significant economic losses to the poultry industry. This study investigated the presence of Cryptosporidium spp. in domestic ducks of family Anatidae (Cairina moschata) from two rustic commercial aviaries located in the city of Rio de Janeiro, Brazil. A total of 315 fecal samples were collected from domestic ducks in two different areas (N=186 in area A and N=129 in area B). The microscopic analysis was conducted using a sugar centrifugal flotation technique for the identification of Cryptosporidium spp. oocysts, followed by PCR/sequencing analyses of the partial sequence of the 18S rDNA gene to determine the Cryptosporidium species. Of the 315 samples collected, only 10 (186/5.38%) from area A were positive for Cryptosporidium. The nucleotide sequence and phylogenetic analyses identified that all samples were identical (100%) and belonged to Cryptosporidium baileyi species, which is closely related to gastric species and of importance in animal health.
Candidate Term Boundary Conflict Reduction Method for Chinese Geological Text Segmentation

Field: Computer Science (Physical Sciences)

Though Chinese word segmentation (CWS) relies heavily on arithmetic power to train huge models and human work to label corpora, models and algorithms are still less accurate, especially for segmentation in a specific domain. In this study, a high-degree-of-freedom-priority candidate term boundary conflict reduction method (HFCR) is proposed to solve the problem of manually setting thresholds on segmentation based on information entropy. We quantify the uncertainty of left and right character connections of candidate terms and then arrange them in descending order for local comparisons to determine term boundaries. Dynamic numerical comparisons are adopted instead of setting a threshold manually and randomly. Experiments show that the average F1-value of CWS for Chinese geological text is higher than 95% and the F1-value for Chinese general datasets is higher than 87%. Compared with representative tokenizers and the SOTA model, our method performs better, which solves the term boundary conflict problem well and has excellent performance on single geological text segmentation without any samples or labels.
Lateral motion pin device for tactile communication: an approach with DC mini-motors

Field: Engineering (Physical Sciences)

This paper introduces a new concept of tactile display based on lateral motion of the contact pins. Unlike traditional tactile devices where pins are arranged in an array and move upwards/downwards, a single row of pins moves laterally on a rail to display tactile information as in a 2D matrix. The advantage of this concept is that a row of N actuators can display some information that has been traditionally done with a matrix of NtimesN actuators. An electromechanical actuator based on miniature DC motors was designed and implemented to create such lateral motion. Both tactile display design and actuation approach are presented and discussed.
The Contribution of Reduced Peak Accrual of Bone and Age-Related Bone Loss to Osteoporosis at the Spine and Hip: Insights from the Daughters of Women with Vertebral or Hip Fractures

Field: Medicine (Health Sciences)

Abstract The genetic hypothesis states that a daughter will resemble her mother by about 50% in a given trait because she shares, on average, half her genes. We used this trait resemblance in mothers and daughters to determine whether abnormalities in volumetric bone mineral density (vBMD) or bone size in women with fractures originate in growth or aging. vBMD and volume of the third lumbar vertebra and femoral neck were estimated using posteroanterior (PA) scanning by dual-energy X-ray absorptiometry (DXA). Vertebral volume was estimated as (scan area)3/2 and femoral neck volume was π ∗︁ (width/2)2 ∗︁ height. vBMD was bone mineral content (BMC)/volume. The data were expressed as age-specific SD or Z scores (mean ± SEM). Vertebral vBMD was reduced by −0.98 ± 0.14 SD (p &lt; 0.001) in 34 women with vertebral fractures, and by −0.36 ± 0.13 SD (p &lt; 0.05) in their 44 premenopausal daughters. The vBMD deficit in the daughters (relative to age-matched controls) was no different from one-half their mothers' deficit (relative to their age-matched controls). Vertebral volume was reduced in the women with vertebral fractures relative to age-matched controls (−0.77 ± 0.15 SD; p &lt; 0.001), but not in their daughters (−0.17 ± 0.13 SD, NS). The 31 women with hip fractures and their 41 premenopausal daughters had no deficits in vertebral volume or vBMD. Femoral neck vBMD was reduced in the women with hip fractures (−1.24 ± 0.12 SD; p &lt; 0.001) but not in their daughters (−0.17 ± 0.13 SD, NS). Femoral neck volume was increased by 0.98 ± 0.30 SD (p &lt; 0.05) in women with hip fractures (relative to age-matched controls) and by 0.54 ± 0.14 SD (p &lt; 0.001) in their daughters (relative to age-matched controls); that is, about one-half that of their mothers. We propose that women with vertebral fractures have reduced vertebral vBMD because of, in large part, reduced accrual of bone during growth (because the deficit in their daughters was almost one-half their mothers' deficit); reduced vertebral volume in women with vertebral fractures is caused by reduced periosteal apposition during aging (because their daughters have no deficit in vertebral volume). Women with hip fractures have reduced vBMD because of age-related bone loss (because their daughters have no deficit in vBMD) but the increased femoral neck volume is growth related (because their daughters' femoral neck size is increased by one-half as much). The pathogenesis of bone fragility at the axial and appendicular skeleton is heterogeneous and has its origins in growth and aging.
Explicit Comprehension Instruction: A Review of Research and a New Conceptualization of Instruction

Field: Arts and Humanities (Social Sciences)

Over the last several years, research in reading comprehension has provided the impetus for changes in our thinking about comprehension instruction. From this research, new instructional frameworks for teaching comprehension have been developed. Studies of instruction confirm that we can do a better job of teaching comprehension by using these new instructional frame-works than by following the traditional basal reading paradigm. This article synthesizes recent research on comprehension instruction and presents a new conceptualization of instruction. Representative instructional studies of inference training, reciprocal teaching, and process training are reviewed. The concept of explicit comprehension instruction is then described and contrasted with more traditional models of direct instruction. Next, potential difficulties in implementing explicit comprehension instruction in classrooms are discussed. Finally, 2 important curricular concerns are raised.
Low Grade Neoplasia And Colorectal (CR) Endoscopic Submucosal Dissection (ESD): Are The Adverse Events Acceptable? Results Of A Prospective Multicentre Registry

Field: Medicine (Health Sciences)

Aims The European Society of Gastrointestinal Endoscopy (ESGE) has recently published a position statement for optical diagnosis suggesting that, for Vienna category (VC)≤ 3 colorectal lesions (CRL), performing EMR would be sufficient therapy. Our aims were: 1.) to assess the ESD complication rates when comparing VC≤ 3 vs. VC≥ 4 CRL and 2.) to compare the overall ESD risk of complications with a previously published Spanish EMR series.
Wine and religion

Field: Arts and Humanities (Social Sciences)

Between 1700 and the present, wine and other alcoholic beverages were challenged by religious movements, beginning with Methodists in the eighteenth century, who saw alcohol as harmful to workers. For the most part, the Catholic Church maintained a positive view of wine, but the Church in France suffered a setback when the French Revolutionary government nationalised and sold all vineyards and other church land in 1790. This ended the centuries-long connection between the Church and wine production in France. The temperance movements of the nineteenth century in the US, Scandinavia and elsewhere were often led by Protestant women who called into question the health and other benefits often claimed for wine. New Christian denominations, such as the Mormons and the Salvation Army, adopted policies of abstinence, and there was a campaign to have mainstream churches use grape juice, rather than wine, in communion services. But it was largely unsuccessful, and during Prohibition in the US, an exemption was made for wine to be produced and sold to Christians and Jews for religious purposes. In the twentieth century, religion played a minor role in alcohol policies. In the 1960s, the Catholic Church began to allow the laity wine at Eucharist, Muslim immigration to Europe had a small impact on wine consumption in Europe and the Arab Spring tightened alcohol policies in some majority-Muslim states.
Distribution of mast cells in relation to Schistosoma japonicum induced lesions in pigs.

Field: Veterinary (Health Sciences)

The pathogenesis of schistosomiasis japonica has been extensively studied, however only little attention has been paid to the presence and localization of mast cells in relation to Schistosoma japonicum induced lesions. The aim of the present pilot study was to assess the parasitological and pathological responses in S. japonicum infected pigs with emphasis on the description of the distribution of mast cells in relation to lesions in the liver and cecum. Six pigs were exposed to 2,000 cercariae and examined 9 weeks post-infection. Three unexposed pigs of the same age served as helminth free controls. All infected pigs developed granulomatous hepatitis and typhlitis. In the liver, the degree of mast cell infiltration was higher in the infected pigs compared to the unexposed control group. This distinction could not be shown in the cecum. In both the liver and cecum, a mild to moderate number of mast cells were present within the granulomas. A significant relation was found between infection with S. japonicum and the mast cell infiltration in the liver. Due to their possible association with hepatic fibrosis, it seems as if they have some function in the fibrogenic process and thereby play a dual role in the pathogenesis of S. japonicum. In conclusion, the results show that mast cells are recruited to egg induced lesions in both the liver and the cecum.
Signal Modeling for Two-Dimensional Image Structures and Scale-Space Based Image Analysis

Field: Computer Science (Physical Sciences)

Model based image representation plays an important role in many computer vision tasks. Consequently, it is of high significance to model image structures with more powerful representation capabilities. In the literature, there exist bulk of researches for intensity based modeling. However, most of them suffer from the illumination variation. On the other hand, phase information, which carries most essential structural information of the original signal, has the advantage of being invariant to the brightness change. Therefore, phase based image analysis is advantageous when compared to purely intensity based approaches. This thesis aims to propose novel image representations for 2D image structures, from which useful local features can be extracted, which are useful for phase based image analysis. The first approach presents a 2D rotationally invariant quadrature filter. This model is able to handle superimposed intrinsically two-dimensional (i2D) patterns with flexible angles of intersection. Hence, it can be regarded as an extension of the structure multivector. The second approach is the monogenic curvature tensor. Coupling methods of differential geometry, tensor algebra, monogenic signal and quadrature filter, we can design a general model for 2D structures as the monogenic extension of a curvature tensor. Based on it, local representations for the intrinsically one-dimensional (i1D) and i2D structures are derived as the monogenic signal and the generalized monogenic curvature signal, respectively. From them, independent features of local amplitude, phase and orientation are simultaneously extracted. Besides, a generalized monogenic curvature scale-space can be built by applying a Poisson kernel to the monogenic curvature tensor. Compared with other related work, the remarkable advantage of our approach lies in the rotationally invariant phase evaluation of 2D structures in a multi-scale framework, which delivers access to phase-based processing in many computer vision tasks. To demonstrate the efficiency and power of the theoretic framework, some computer vision applications are presented, which include the phase based image reconstruction, detecting i2D image structures using local phase and monogenic curvature tensor for optical flow estimation.
Differential scanning calorimetry as a powerful tool for investigation of solid-phase transformations in heating, isothermal annealing and cooling

Field: Materials Science (Physical Sciences)

Solid-solid phase transformations play an important role for the adjustment of machining- and application-properties of metallic materials. During recent years, we developed advanced techniques to analyze solid-solid phase transformation by DSC in a very wide dynamic range. This talk will introduce these techniques, using reactions in aluminium alloys as examples. To achieve the required high dynamic range during cooling we combine three different indirect and direct measuring techniques and five types of DSC devices. Nowadays physically-based models verified with our DSC results moreover allow to predict precipitation volume fractions, solute mass fractions. Latest results on property predictions as function of cooling rate will be presented.
Guinea Pigs

Field: Medicine (Health Sciences)

Abstract This chapter addresses the use of radioisotopes in medical research, where the use of human subjects raised new ethical problems. It features examples from physiology and endocrinology, where radioisotopes were used to investigate the absorption and movement of micronutrients and the regulation of hormones. The first case concerns the use of iron-59 in studies of mammalian metabolism of this element. An outgrowth of this line of research included controversial studies of iron metabolism in pregnant women that took place at Vanderbilt in the 1950s. The second case examines the development of radioimmunoassays, in which research on the clinical use of radioiodine in a Veterans Administration Hospital led Rosalyn Yalow and Solomon Berson to develop a diagnostic method with wide applicability, including in basic research.
Medication review with follow-up service by community pharmacists forpatients under treatment with coumarin anticoagulants in collaboration with Primary Care

Field: Health Professions (Health Sciences)

Abstract Introduction: Anticoagulation treatment with VKA presents an optimal risk-benefit balance in patients with a Time in Therapeutic Range (TTR) >70%. Pharmacist integration in the primary health care team, using innovative tools such as the SAME-TT2R2 and pharmacogenetics information, could enhance the management of anticoagulated patients. This study aims to assess the effectiveness of a medication review with follow up service by community pharmacists, in collaboration with Primary Care for patients treated with VKA. Methods and analysis: A randomized controlled study with blinded outcome assessment will be conducted. Patients treated with VKA with TTR<70% from 2 health care centres will be included. Primary outcome is TTR during last 6 months. Secondary outcomes will be: adherence, vitamin K intake, patient’s knowledge, pharmacogenetics and SAME-TT2R2’s clinical utility, costs, quality of life and satisfaction. Potential clinical, economic, and humanistic impact of the interventions will be retrospectively analysed using CLEO tool. Intervention group will receive a medication review with follow up, physicians will receive an evidence-based report patient´s medicine-related problems, genetic and clinical limitations for the use of VKA. Patients will be followed for 6 months. Sample size: 130 patients will be recruited for 90% power based on the most conservative scenarios. Multivariate, cost-effectiveness analyses will be used. Ethics and dissemination: The study design was approved by the ethical committee of Aragon. The trial is registered at Clinical Trials.gov dated 25/05/2017: NCT03154489. Trial results will be published in peer-reviewed journals and at conferences.
Cell division in placentas of appropriate and small-for-gestational-age infants. A flow cytometry study.

Field: Medicine (Health Sciences)

Cell division in the placenta is maintained until and beyond term. Placentas of SGA infants have on average, lower proliferative activity than placentas of non-SGA infants, but the difference is too small to be of predictive value in identifying intrauterine growth retardation.
Unusual Lipid Components of Legionella gormanii Membranes

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

Legionella spp. cause Legionnaires’ disease with pneumonia as the predominant clinical symptom. L. gormanii is the second most prevalent causative agent of community-acquired pneumonia after L. pneumophila. The study aimed to characterize the lipidome of L. gormanii membranes and the importance of these analyses in bacterial chemotaxonomy. Lipidomic analyses based on ultra-high performance liquid chromatography-mass spectrometry allowed the detection of individual molecular species of a wide range of L. gormanii membrane lipids contained in the outer (OM) and inner membranes (IM). The lipid profile comprised glycerolipids (triglycerides, diglycerides), phospholipids (phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, cardiolipin), and sphingolipids (ceramides, hexosylceramides). The most abundant lipid fraction in the IM and OM were phospholipids. The lipidomic analysis showed that two independent phosphatidylcholine (PC) synthesis pathways operating in L. gormanii: the PE-methylation (PmtA) pathway and the PC synthase (Pcs) pathway. Comparison of the molecular profile of PC species contained in the lipids of L. gormanii membranes cultured on the medium, with and without exogenous choline, showed quantitative differences in the PC pool. An unusual feature of the L. gormanii lipids was the presence of ceramides and hexosylceramides, which are typical components of eukaryotic cells and a very small group of bacteria. To the best of our knowledge, this is the first report of the occurrence of ceramides in Legionella bacteria.