jimnoneill/paper-to-field-training huggingface dataset:
Identification and Analysis of Key Genes Associated with Ulcerative Colitis by Integrated Bioinformatics Methods

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

Abstract Background: Ulcerative colitis (UC) is a prevalent inflammatory bowel disease of the colonic mucosa. The exact mechanism of the disease still remains unclear. Here we tried to explore new biomarkers and potential therapeutic targets in UC through adopting integrated bioinformatics tools.Results: By performing DEGs analysis, 59 upregulated and 39 downregulated DEGs were successfully identified from GSE3365, respectively. And they were mainly enriched in the terms of Cytokine-cytokine receptor interaction,Viral protein interaction with cytokine and cytokine receptor,Pantothenate and CoA biosynthesis,IL-17 signaling pathway and Chemokine signaling pathway. Based on the data of protein–protein interaction (PPI), the top 10 hub genes were ranked, including Growth-regulated alpha protein (CXCL1), C-C motif chemokine 2 (CCL2), C-X-C chemokine receptor type 1 (CXCR1), Low affinity immunoglobulin gamma Fc region receptor III-B (FCGR3B), C-X-C chemokine receptor type 2 (CXCR2), Prostaglandin G/H synthase 2 (PTGS2), Triggering receptor expressed on myeloid cells 1 (TREM1), Interleukin-1 receptor type 1 (IL1R1), fMet-Leu-Phe receptor (FPR1), and Band 3 anion transport protein (SLC4A1).What’s more, the results of correlation analysis demonstrated that there was a positive correlation between the 10 hub DEGs.Conclusion: Ten DEGs were identified as potential candidate diagnostic biomarkers for patients with UC in present study. However, further experiments are needed to confirm the functional pathways and hub genes associated with UC.
Improving selection practices of subcontractors on building construction project in Nigeria

Field: Engineering (Physical Sciences)

Subcontracting in Nigeria has extensively been used in the construction industry. It allows main contractor to employ a minimum workforce in construction projects and promotes specialization. The relationship between the main contractor and the subcontractors differ from one project to another. However, improper selection of subcontractors might lead to many problems during work pogress. This research focuses on improving subcontractor selection practices by the main contractors on building construction project in Nigeria. The objectives of the research were to identify the factors causing adversarial relationship between the main contractor and the subcontractor, identify significant factors used for subcontractors selection by the main contractor, and recommend ways for improving a better selection practices of subcontractors by the main contractor. The quantitative approach was used to obtain information from contractors (category A) for subcontractors selection practices. The data from the questionnaires were collected and analysed using Statistical Package for Social Science (SPSS) version 22.0. The data gathered was \nf converted into the form of percentages, tables, and charts. The results of the indings shows that incompetency of the subcontractor and non adherence of the subcontractor to the time schedule where among the factors causing adversarial relationship between the main contractor and the subcontractor, while providing dequate inormation to the subcontractor and speciality in certain type of work were ranked top for the factors used for subcontractors selection by the main contractor. In addition avoiding collection of kickbacks in construction and use of skilled labour force were the most significant ways to improve subcontractors selection practices by the main contractor. Subcontractors selection plays a vital role in the overall success of any construction project in order to get best results in te1ms of cost, time, and quality for the projects
A self-organizing neural network approach for the identification of motifs with insertions and deletions in protein sequences

Field: Computer Science (Physical Sciences)

Current popular algorithms of motif identification in protein sequences face two difficulties, large computation and insertions and deletions of letters. In this paper, we provide a new strategy that solves this problem in a more efficient and effective way. We build a self-organizing neural network with multiple levels of subnetworks to classify subsequences obtained from the protein sequences. We maintain a low computational complexity through the use of this multi-level structure so that the classification of each subsequence is performed with respect to a small subspace of the whole input space. The new definition of pairwise distance between motif patterns provided in this paper can deal with more insertions/deletions allowed in a motif than other algorithms. In the simulation result, our algorithm significantly outperforms existing algorithms in both accuracy and reliability aspects.
Simulation of Logistic Port Processes

Field: Decision Sciences (Social Sciences)

The Prosim simulation model is capable of conducting simulation of a wide variety of logistic processes. Application of the model is especially powerful when a large number of parallel and interrelated parameters is concerned. Typical applications include port and terminal operations, ranging from nautical issues to berth occupancy planning and sizing of port facilities. Similarly, simulations of cargo flows, product deliveries and onward transportation options can permit sizing and layout planning for on-land facilities. The Prosim model consists of a description of all relevant variables, and the way they are interrelated with other variables inside or outside the model. Input required for the model can be separated in two groups, physical parameters and process description. Physical input parameters define the physical characteristics of the simulated process, and can be fixed, variable or randomly generated. Process descriptions define the behavior of the system, often consisting of logistic decisions or checks that must be made.
Supplementary Material 1 - Supplemental material for Pediatric Hidradenitis Suppurativa: A Cross-Sectional Study on Clinical Features and Treatment Approaches

Field: Medicine (Health Sciences)

Supplemental material, Supplementary Material 1, for Pediatric Hidradenitis Suppurativa: A Cross-Sectional Study on Clinical Features and Treatment Approaches by Simone Garcovich, Luca Fania, Dante Caposiena, Giulia Giovanardi, Andrea Chiricozzi, Clara De Simone, Chiara Tartaglia, Davide Ciccone, Luca Bianchi, Damiano Abeni and Ketty Peris in Journal of Cutaneous Medicine and Surgery
A Study of Linkage Relationships of Blood Group P with Naked Neck, Silkie Feathering, and Recessive White in Chicken

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

Linkage relationships of blood group P (Ea-P), naked neck (Na), silkie feathering (h), and recessive white plumage (c) were studied to attempt to clarify the h-Na-Ea-P region of linkage group III of the chicken. The Na-Ea-P linkage values obtained in this test agreed with previous reports, and pooled data were used to recalculate a map distance of 27.9 +/- 2.3 map units between these two loci. A significant chi square for linkage was calculated between Na and c; however, because of the relatively low numbers of progeny tested, the high linkage value calculated, and the absence of detectable linkage between c and the other marker genes, this was probably a chance deviation. All other linkage relationships appeared negative, supporting the current suggested linear order of these loci as h-Na-Ea-P with c not being in this chromosomal region.
Molecular dynamics study of iron at Earth’s inner core condition

Field: Physics and Astronomy (Physical Sciences)

The molecular dynamics (MD) simulation is applied to predicting the structure and physical properties of iron in the earth’s inner core. The potential energy of iron is approximated as the sum of (1) a volume‐dependent term resulting from the conduction electrons, (2) a structure‐dependent term from pair interactions between Fe ions, and (3) the thermal excitation energy of the conduction electrons. The MD predicted densities, bulk moduli, and rigidities of ε‐Fe at earth’s inner core conditions are compared with the seismological models, to give constraints on the inner core composition and temperature. The MD simulation is further used to investigate the possible existence of another dense phase at the ultra‐high pressures and high temperatures in the inner core.
The successful use of subcutaneous abatacept in refractory anti- human transcriptional intermediary factor 1-gamma dermatomyositis skin and oesphagopharyngeal disease

Field: Medicine (Health Sciences)

The successful use of subcutaneous abatacept in refractory anti-human transcriptional intermediary factor 1-gamma dermatomyositis skin and oesphagopharyngeal disease Rheumatology key message. Subcutaneous abatacept may be an effective treatment in dermatomyositis patients with refractory skin and oesophageal disease.
La négociation des plaidoyers de culpabilité : une pratique hétérogène

Field: Social Sciences (Social Sciences)

This article presents the principal results of a study on plea bargaining at the Montreal Justice Hall. Various methods were adopted: observations, a thorough study of the files, interviews and analyses of the judicial statistics. The results show that negotiations vary considerably depending on the gravity of the offence concerned. In the case of a minor charge or a murder charge, the characteristics as well as the stakes and consequences of the plea bargaining are very different. In minor cases, the negotiations are reduced to their simplest form. They are a routine process of cooperation between the parties rather than bargaining to get an admission of guilt by promising the accused a reduced charge or sentence. On the contrary, the negotiations in murder cases take the traditional form of plea bargaining in which the power struggle is dominant. The study shows that it is in cases of murder than plea bargaining presents most difficulties.
The Sulu Sea

Field: Social Sciences (Social Sciences)

Spain never managed to take control of the Sulu Archipelago, where the Sulu Sultanate thrived, particularly after c.1770, on a combination of trade and slave raiding. Maritime raiding was a central means of warfare for both the Sulu Sultanate and Spain during the protracted Moro Wars from 1565 to 1876, but from the second half of the eighteenth century, Spain began increasingly to label their adversaries 'pirates'. From the 1840s the Spanish Navy began to gain the upper hand in the struggle at sea, leading to a sharp decline in large-scale piracy and coastal raiding from the middle of the century. The lack of international recognition of Spain's territorial claims over the Sulu Sultanate, however, hindered naval cooperation with the British and the Dutch for the purpose of suppressing piracy, which allowed petty piratical activity emanating from the Sulu Sea to continue. The United States took over Spain's colony in the Philippines in 1899 and managed initially to maintain reasonable maritime security, although attacks against indigenous fishermen and Chinese traders and pearl fishers continued. Between 1907 and 1909 the last serious outbreak of piracy in the area occurred with the depredations of Jikiri and his band, which the Americans only defeated with considerable difficulty.
Symptomatic left temporal arteriovenous traumatic fistula

Field: Medicine (Health Sciences)

Symptomatic left temporal arteriovenous traumatic fistulaA 25-year-old right-handed man presented with left greater than right tinnitus several months after receiving a blow to the left temporal area.Bruit was noted during auscultation.CT angiography (figure 1) and catheter angiography (figure 2, A and B) showed a traumatic left scalp arteriovenous fistula.The fistula was fed by an enlarged left superficial temporal artery and by hypertrophic branches of the occipital artery (figure 2, A andB).There was also recruitment of contralateral external carotid branches.Therapeutic options include surgical or endovascular disconnection of the fistula. 1 The patient underwent Onyx and coil embolization of the fistula with complete obliteration (figure 2C) and resolution of the bruit.Scalp arteriovenous fistulas can result from blunt trauma. 1 Obliteration of the fistulous connections and of the proximal portion of the draining vein is the mainstay of endovascular therapy to prevent recurrence. 2
INTERVERTEBRAL DISC DEGENERATION LINKED TO STRUCTURAL GENE VARIATIONS

Field: Medicine (Health Sciences)

During the recent past focus has shifted from identifying intervertebral disc degeneration as being caused by physical exposure and strain to being linked with a variety of genetic variations. The objective of this review is to provide an up to date review of the existing research data regarding the relation of intervertebral disc degeneration to structural protein genes and their polymorphisms and thus help clearly establish further avenues where research into causation and treatment is needed. A comprehensive search using the keywords “Collagen”, “COL”, “Aggrecan”, “AGC”, “IVDD”, “intervertebral disc degeneration”, and “lumbar disc degeneration” from PubMed and Google Scholar, where literature in the English language was selected spanning from 1991 to 2019. There are many genes involved in the production of structural components of an intervertebral disc. The issues in production of these components involve the over-expression or under-expression of their genes, and single nucleotide polymorphisms and variable number of tandem repeats affecting their structures. These structural genes include primarily the collagen and the aggrecan genes. While genetic and environmental factors all come into play with a disease process like disc degeneration, the bulk of research now shows the significantly larger impact of hereditary over exposure. While further research is needed into some of the lesser studied genes linked to IVDD and also the racial variations in genetic makeup, the focus in the near future should be on establishment of genetic testing to identify individuals at greater risk of disease and deliberation regarding the use of gene therapy to prevent disc degeneration.
The Factor Inhibiting HIF Asparaginyl Hydroxylase Regulates Oxidative Metabolism and Accelerates Metabolic Adaptation to Hypoxia

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

Animals require an immediate response to oxygen availability to allow rapid shifts between oxidative and glycolytic metabolism. These metabolic shifts are highly regulated by the HIF transcription factor. The factor inhibiting HIF (FIH) is an asparaginyl hydroxylase that controls HIF transcriptional activity in an oxygen-dependent manner. We show here that FIH loss increases oxidative metabolism, while also increasing glycolytic capacity, and that this gives rise to an increase in oxygen consumption. We further show that the loss of FIH acts to accelerate the cellular metabolic response to hypoxia. Skeletal muscle expresses 50-fold higher levels of FIH than other tissues: we analyzed skeletal muscle FIH mutants and found a decreased metabolic efficiency, correlated with an increased oxidative rate and an increased rate of hypoxic response. We find that FIH, through its regulation of oxidation, acts in concert with the PHD/vHL pathway to accelerate HIF-mediated metabolic responses to hypoxia.
A Prototype For Quantum Database in Hybrid Quantum

Field: Computer Science (Physical Sciences)

<p>This study proposes a prototype And a possibility to converge both classical database and fully quantum database. This study mostly identifies the gap between this classical database and quantum database and it proposes a hypothesis and prototype which can be implemented in future products. It is a way that can be used in future industrial product development on hybrid quantum computers. The existing concept used to consider oracle as a black box this study opens up the possibility for the quantum industry to develop the QASAM module so that we can develop a fully quantum database instead of using a classical database as BlackBox. As the Toffoli gate is basically an effective NAND gate it is possible to run any algorithm theoretically in quantum computers. So we will propose a logical design for memory management for the quantum database, security enhancement model, Quantum Recovery Manager & automatic storage management model and more for the quantum database which will ensure the quantum advantages. In this study, we will also explain the Quantum Vector Database as well as the possibility of improvement in duality quantum computing. It opens up a new scope, possibilities and research area in a new approach for quantum database and duality quantum computing.</p>
Forced and Ambient Vibration Tests and Vibration Monitoring of Hakucho Suspension Bridge

Field: Engineering (Physical Sciences)

Forced and ambient dynamic tests of the Hakucho Bridge were carried out to study the dynamic characteristics of this suspension bridge. Dense-array measurement was employed in order to capture not only natural frequencies and damping, but also the mode shapes of the bridge. The natural frequencies and mode shapes obtained from the forced and ambient vibration tests agreed well with those calculated by a three-dimensional finite element model. A new method that combines the random decrement method with the Ibrahim time domain method is proposed to systematically identify the natural frequencies, damping, and mode shapes. This method is successfully applied to ambient vibration data. It is shown that the natural frequency of the first vertical bending mode decreases noticeably as the wind speed increases. It is also shown that the shape of the first vertical bending mode changes slightly near the towers, depending on the wind velocity; this finding indicates that the change may be associated with friction in the bearings at the towers. Finally, application of the Global Positioning System to measure static displacement of the girder is explained.
Six-month gain in weight, height, and CD4 predict subsequent antiretroviral treatment responses in HIV-infected South African children

Field: Medicine (Health Sciences)

Construct percentile curves for 6-month gain in weight, height, CD4 cell count, and CD4 percentage (CD4%) in children initiating ART, and to assess the association between lower percentiles and subsequent ART responses. Cohort of 1394 HIV-infected children initiating ART between April 2004 and March 2008, Johannesburg, South Africa The generalized additive model for location, scale, and shape was used to construct percentile curves for 6-month gain in weight, height, CD4 cell count, and CD4%. Cox proportional models were used to assess the association between lower percentiles of each distribution and death, virological suppression, and treatment failure between 6 to 36 months post-ART initiation. Lower percentiles for gain in weight, CD4, and CD4% count after 6 months of ART, but not height, were associated with poor subsequent treatment outcomes independent of baseline characteristics, with increasing strength of association as percentiles decreased. Age-specific 6-month post-ART weight gain in our cohort was substantially higher compared with 6-month weight gain in non-HIV-infected American children of the Fels Institute cohort and the attained weight-for-age at 6 months post-ART plotted on WHO weight-for-age growth charts were not associated with subsequent treatment outcomes. Gain in CD4% in the first 6 months of ART was the best predictor of poor subsequent ART outcomes. In areas with limited access to CD4%, weight gain post-ART using our newly developed reference distributions for HIV-infected children on ART is a good alternative to CD4%, and clearly superior to the commonly used 'Road-to-Health' weight-for-age charts.
A neural network based method for part demands prediction in auto aftermarket

Field: Computer Science (Physical Sciences)

In the supply chain management of auto aftermarket, companies strive to manage inventory with low cost while maintaining a reasonable order fulfillment rate. To achieve this objective, a critical issue is to predict the demand for auto parts with high accuracy. Based on the factors relevant to auto aftermarket, this paper proposed an artificial neural network based method to forecast the demands of auto parts. The effectiveness of the proposed method is illustrated with a case study of an auto 4s shop in Shanghai.
Synergy of Education, Dakwah, and Social as Capital for Implementing Islamic Education In The Era of Collaboration (Field Study at YPI Al Azhar Jakarta)

Field: Arts and Humanities (Social Sciences)

The ideal educational process is education that is able to combine knowledge, attitudes and skills for students. Apart from understanding knowledge, students are able to practice and implement their knowledge in everyday life. In reality, educational institutions, especially Islamic educational institutions, need good strategies so that the schools they manage can truly become a place for deepening knowledge and implementing morals for all learners. Institutions providing Islamic education that already have da'wah and social units or divisions, especially those whose governance is still partial, can use this research as a reference. This research was conducted at YPI Al Azhar, an Islamic education provider institution that has been operating for 72 years. YPI Al Azhar has an education unit, a da'wah and social unit, and other units in its organizational structure and governance. The IN units stand individually, but are packaged in program synergy and collaboration. The curriculum, which has been prepared with the development of internal needs, is packaged in such a way that it includes activities for implementing da'wah and social activities for students. This is in line with programs and activities in the Da'wah and Social Units. Even though it is managed by each unit, schools and students are directly involved in da'wah and social activities. In the end, students can directly implement da'wah and social values to the community. Activities for renovating places of worship, establishing Saung Ilmu in underdeveloped villages, creating public facilities, providing scholarships for non-formal education students can be carried out optimally by students. The result is that students can use the program as a bridge for implementing morals and morality among others. School activities that intersect with da'wah and social activities can be carried out well through synergy and collaboration. This has a positive impact on public trust, thus influencing the target for New Student Admissions in each academic year.
CRANKING THE CHIRAL SOLITON BAG MODEL: QUANTUM CORRECTIONS

Field: Physics and Astronomy (Physical Sciences)

The generation of physical states from mean field hedgehogs by cranking is extended to coherent hedgehogs, thus improving the agreement between the cranking and coherent state projection methods, and enabling us to correct simultaneously for translational and rotational fluctuations. These corrections lead to a drastic reduction in the mean nucleon-delta mass which, for the physical values of m π and F π , is lower than, or approximately equal to, the experimental value.