jimnoneill/paper-to-field-training huggingface dataset:
From drug resistance mechanisms to microRNA function in melanoma

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

Cutaneous melanoma is an aggressive skin cancer that emerges from the unrestrained proliferation of melanocytes, which are the pigment producing cells in the basal layer of the epidermis. Despite the fact that it only accounts for approximately 5% of all skin cancers, melanoma is responsible for the vast majority of skin cancer-related deaths. As more than half of the patients with sporadic melanoma harbour activating mutations in the protein kinase BRAF, the development of small kinase inhibitors targeting mutated BRAF led to an increased overall survival of patients with metastatic melanoma. Despite the initially promising results, the rapidly emerging resistance to these targeted therapies remains a serious clinical issue. To investigate the mechanisms underlying resistance to targeted therapies, we used in vitro BRAF-mutant drug-sensitive and drug-resistant melanoma cell models that were generated in our laboratory. First, we performed a kinase inhibitor library screening with the aim to identify novel kinase inhibitor combinations to circumvent or delay BRAF inhibitor-induced resistance. We have characterised synergistic kinase inhibitors targeting the MAPK pathway and the cell cycle showing promising effects in BRAF-mutant drug-sensitive and -resistant cells, which could be used as an effective sequential or alternative treatment option for late-stage melanoma patients. Additionally, we investigated the impact of BRAF inhibitors at the transcriptional level by comparing miRNome and transcriptome changes in drug-sensitive and -resistant melanoma cells. We identified miRNAs (e.g. miR-509, miR-708) and genes (e.g. PCSK2, AXL) that were distinctly differentially expressed in resistant compared to sensitive cells. Subsequent co-expression analyses revealed a low MITF/AXL ratio in a subset of resistant cell lines, suggesting that miRNAs might be involved in the switch from one molecular phenotype to another, thus conferring tolerance to targeted therapies. Finally, we applied a method based on cross-linking ligation and sequencing of hybrids (qCLASH) to provide a comprehensive snapshot of the miRNA targetome in our BRAF-mutant melanoma cells. To our knowledge, we implemented for the first time a CLASH-based method to cancer cells, and identified over 8k direct and distinct miRNA-target interactions in melanoma cells, including many with non-predicted and non-canonical binding characteristics, thus expanding the pool of miRNA-target interactions. Taken together, these results provide new insights into complex and heterogeneous responses to BRAF inhibition, adding an additional level of complexity to drug-induced (post-) transcriptional network rewiring in melanoma.
Vancomycin‐soaked femoral head allograft in opening wedge high tibia osteotomy enables earlier postoperative recovery and reduces infection rates compared to allogenic bone chips

Field: Medicine (Health Sciences)

Abstract Purpose To investigate the benefits of vancomycin‐soaked femoral head allograft versus allogenic bone chips as an osteotomy gap filler in reducing infection rates and perioperative pain control after medial opening wedge high tibial osteotomy (MOW‐HTO). Methods Retrospective analysis of 114 knees that underwent MOW‐HTO between 2013 and 2020. Osteotomy gaps were filled with vancomycin‐soaked femoral head allograft (Study Group) or allogenic bone chips (Control Group). Both groups received systemic antibiotics. Perioperative parameters studied included pain, blood loss, length of stay, postoperative day (POD1) pain scores at rest, with activity as well as ambulatory distance. Patients in the Study Group were also followed up prospectively and clinical outcome scores, namely Knee Society Score, Oxford knee score (OKS) and Physical and Mental Component of the Short‐Form 36 Questionnaire (PCS and MCS, respectively). Statistical analyses using Student’s T ‐test were performed between the groups. Results Patients of the study group had significantly better POD1 visual analogue scale (VAS) at rest (0.9 ± 1.6 vs 2.9 ± 1.2, p < 0.001) as well as when active (3.0 ± 1.9 vs 5.8 ± 1.5, p < 0.001). A greater proportion of patients in the study group ambulated on POD 1, (90.6% vs 26.0%, p < 0.001). Of those who ambulated on POD1, study group patients managed to cover a greater ambulatory distance (13.9 ± 7.4 m vs 8.4 ± 9.3 m, p < 0.05). The proportion of study group patients requiring patient‐controlled analgesia (PCA) was also significantly less compared to the control group (32.8% vs 58.0%, p < 0.05). Of those requiring PCA, the amount of morphine requirement was also significantly reduced in the group with vancomycin‐soaked allograft (8.7 ± 8.1 mg vs 23.9 ± 33.0 mg, p < 0.05). The study group also had a reduced length of stay (3.5 ± 2.0 days vs 5.5 ± 2.6 days, p < 0.001). Patients in the study group demonstrated significant improvement in Knee Society Knee Score (KSKS), OKS, PCS and MCS at 12 months postoperatively. The study group had a significantly reduced incidence of superficial wound infections compared to the control group (3.1% vs 18.0%, p < 0.05). Conclusion Vancomycin‐soaked femoral head allograft reduced superficial and deep wound infections in MOW‐HTO. It was also effective in reducing postoperative pain, thereby enabling early ambulation and shorter hospital stays. Level of evidence Retrospective comparative study, III.
An Adaptive Optics Survey of M6.0–M7.5 Stars: Discovery of Three Very Low Mass Binary Systems Including Two Probable Hyades Members

Field: Physics and Astronomy (Physical Sciences)

A survey of 30 nearby M6.0-M7.5 dwarfs with Ks<12 mag utilizing the Hokupa'a adaptive optics system at the Gemini North Telescope has discovered 3 new binary systems. All 3 systems have separations between 0.12-0.29 arcsec (3-10 AU) with similar mass ratios (q>0.8, Delta Ks<0.7). This result gives further support to the suggestion that wide (a>20 AU) very low mass (M_{tot}<0.185 M_sun) binary systems are exceedingly rare or perhaps even non-existant. The semimajor axis distribution of these systems peaks at ~5 AU, tighter than more massive M and G binary distributions which have a broad peak at separations of \~30 AU. We find a sensitivity-corrected binary fraction in the range of 5_{-2}^{+4}% for M6.0-M7.5 stars with separations a>3 AU. This binary frequency is less than the ~32% measured among early M dwarfs over the same separation range. Two of the low-mass binaries are probable Hyades open cluster members based on proper motions, cluster membership probabilities, radial velocities, and near-IR photometry. LP415-20 has the distinction of being the tightest (3.6 AU) multiple system ever spatially resolved in the cluster and the companions of LP415-20 and LP475-855 are among the least massive objects ever resolved in the Hyades with estimated masses of 0.081_{-0.010}^{+0.009} and 0.082_{-0.009}^{+0.009} M_{\sun}.
Occurrence Download

Field: Earth and Planetary Sciences (Physical Sciences)

A dataset containing 58774 species occurrences available in GBIF matching the query: { "and" : [ "TaxonKey is one of (Dryopteris remota (A.Braun ex Döll) Druce, Anemone baldensis L., Cardamine amara subsp. amara, Tyto alba (Scopoli, 1769), Ranunculus bulbosus L., Salix pentandra L., Dianthus superbus subsp. superbus, Tilia cordata Mill., Verbascum thapsus L., Pedicularis ascendens Schleich. ex Gaudin)", "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,\n 3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741,\n 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,\n 28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,\n 30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,\n 40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,\n 31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,\n 27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,\n 31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,\n 14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,\n -21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))", "HasCoordinate is true", "HasGeospatialIssue is false", "Year is greater than or equal to 2019", "Year is less than or equal to 2020" ] } The dataset includes 58774 records from 125 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003949-210914110416597/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.
Macroeconomic Shocks and Labor Supply in Emerging Countries. Some Lessons from Turkey∗

Field: Economics, Econometrics and Finance (Social Sciences)

We investigate the general equilibrium effects of minimum con-sumption constraints over labor supply decisions. Within a simple static model, a minimum consumption constraint modifies labor sup-ply decisions of unskilled workers, generating the well-known added worker effect. The results of the model help to analyze the Turkish labor market where added worker effects were observed following the 2001 crisis. We investigate the asymmetric effects of the crisis, using the Household Budget Surveys that cover the period between 2002 and 2005. The substantial decrease in real wages has increased labor supply for unskilled labor, especially for women.
Internet Entrepreneurship and Economic Growth

Field: Economics, Econometrics and Finance (Social Sciences)

This paper looks at national attempts to promote economic growth through the Internet. Growth can be driven through service exports or internally through increased service transactions and fostering entrepreneurship. India is often held as an example of service exports, but economic statistics show that India might not be a good example for other nations because net service trade is negative and wages have been economically distorted. Ultimately, developing nations need to find internal growth models. Internal growth could be driven though increased consumption due to improved information, or increased investment expenditures from infrastructure investments.
Title "&#963;&#969;&#964;&#942;&#961;" in Ancient Culture and Biblical Discourse: on the problem of semantic evolution of the concept

Field: Arts and Humanities (Social Sciences)

The article is devoted to the problem of semantic evolution of pagan terminology in Christian theology. A specific token becomes the subject of consideration "&#963;&#969;&#964;&#942;&#961;", which has gone through a long history of semantic transformation: from the savior to earthly adversities and misfortunes in the pagan world (natural objects, people, mythological creatures could act as saviors and even the gods) to the Savior of human souls in Christianity. The authors demonstrate how the content of the concept was modified and how, along with the religious meaning, a political component emerged and established itself in the structure of meaning by the Hellenistic era, and then was again pushed into the background. It is suggested that the political connotations are caused not so much by the "power ambitions" of the Church, but, firstly, by the socio-cultural context in which Christianity arose, and, secondly, by the specifics of the pagan worldview in which the idea of sacralizing power was rooted. The task of the authors, who worked with rather archaic material, was not only to reveal the logic of semantic shifts, to understand how Christian theology could become heard in the space of pagan culture. The authors believe that the success of Christian preaching was not least due to the cognitive strategies chosen by the Church, which were directly poisoned by pagan concepts in the work.
Chronic inflammatory back pain commencing late in life: a neglected concept

Field: Medicine (Health Sciences)

Abstract Chronic inflammatory back pain (CIBP) occurs in up to one‐third of those with chronic back pain. Criteria for diagnosis of inflammatory back pain include an onset below 50 years. Using the US National Health and Nutrition Examination Survey data for 2009–2010, we showed that 3% of adults aged 50–69 years have features of CIBP with onset on or after 50 years. There is little information in the literature on CIBP of late onset. Patients with late onset CIBP may be falling through the cracks.
Estimating Aboriginal American Population

Field: Social Sciences (Social Sciences)

This chapter attempts to analyze some major methodological reasons why estimates of aboriginal American population have yielded a picture of small scale preconquest human population in the Western Hemisphere. Angel Rosenblat arrived at a hemisphere-wide estimate of 13,385,000 Indians for 1492, taking that date to represent preconquest conditions. Some form of projection of population figures for small, more intensively studied areas to larger, less well-studied areas of the New World is the method by which a number of Americanists have estimated aboriginal population. Estimates obtained by projecting backward through time population data from modern Indian census counts are seriously defective, as are past applications of the dead reckoning mode of estimation. Ethnohistorical estimations based on careful cross-checking of direct and indirect sources of population data demonstrate that contemporary observers underreported the true magnitude of Native American populations.
Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S7, Table S1, Table S2, Table S3, Table S4 from Cancer-Associated Fibroblasts Affect Intratumoral CD8<sup>+</sup> and FoxP3<sup>+</sup> T Cells Via IL6 in the Tumor Microenvironment

Field: Medicine (Health Sciences)

<p>Supplementary Figure 1. Subgroup analysis of TILs in intra-tumoral tissues according to UICC Stage. Supplementary Figure 2. Correlation between CAFs and ratios of peri- to intra-tumoral of CD8+ or FoxP3+ TILs. Supplementary Figure 3. Quantification of cytokines secreted into cell culture supernatants. Supplementary Figure 4. Fibroblasts and cancer cells cooperate to promote the release of IL-6 in human-derived esophageal cancer cell line. Supplementary Figure 5. IL-6 suppresses tumor immunity of SCCVII subcutaneous tumors in C3H/HeJ mice. Supplementary Figure 6. Correlation between IL-6 staining and αSMA+ CAFs in human esophageal cancer specimens. Supplementary Figure 7. Correlation among αSMA+ CAFs, IL-6 and hypoxia conditions in human esophageal cancer specimens Supplementary Table 1. Correlation between CD8+ or FoxP3+ TILs and clinicopathological characteristics of esophageal cancer. Supplementary Table 2. Univariate analysis of pathologic features and tumorinfiltrating lymphocytes for OS and DFS in esophageal cancer. Supplementary Table 3. Univariate analysis of OS and DFS in the subgroups in intratumoral tissues. Supplementary Table 4. Multivariate analysis of CD8+ and FoxP3+ TILs for OS and DFS in esophageal cancer.</p>
Enabling Cold-Formed Steel System Design through New AISI Standards

Field: Engineering (Physical Sciences)

The objective of this paper is to introduce several new and updated AISI standards for cold-formed steel structural design and explain how these standards provide an evolution for cold-formed steel towards the design of systems instead of isolated members and connections. Cold-formed steel members are used in a wide variety of applications and the historical approach of the AISI standards was primarily to support the design of individual members and steel-to-steel connections. However, as the use of cold-formed steel has expanded and matured it is now possible in several cases to reliably define cold-formed steel systems that are in common use. To support these systems, cold-formed steel framing, metal building secondary systems, steel diaphragm systems, etc. AISI standards now provide system specific design specifications and test standards. The evolution of these standards and the latest versions are explained herein. The focus of the discussion is on why the standards are provided, and how they aim to enable the cold-formed steel engineer, rather than on the specifics of each new edition of the standard. The base standard for all the system specific efforts: AISI S100 is also being reorganized and updated to accommodate new research and this new evolution in cold-formed steel system design. Significant work remains to fully develop cold-formed steel system design and evolve it further towards performance-based standards, but the new suite of AISI standards provides a robust foundation for this effort.
Effect of Spiritual Intelligence on Leadership Effectiveness and Food-hygiene Practices

Field: Social Sciences (Social Sciences)

This study suggests an effort through a Holistic View of spiritual intelligence to address low-quality food problem at public institutions in East Malaysia. It explored the causal relationship of this value to Food Performance, Leadership Effectiveness, and Food-Hygiene Practice through 210 food handlers. The Partial Least Square Structural Equation Modeling (PLS-SEM) was used to test the relationship. Holistic View was found to have a positively significant relationship with the performance but, not Leadership Effectiveness. Holistic View among food handlers was found unaffected by Food hygiene practices.
The epithelial sodium/proton exchanger, NHE3, is necessary for renal and intestinal calcium (re)absorption

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

Passive paracellular proximal tubular (PT) and intestinal calcium (Ca 2+ ) fluxes have been linked to active sodium (re)absorption. Although the epithelial sodium/proton exchanger, NHE3, mediates apical sodium entry at both these sites, its role in Ca 2+ homeostasis remains unclear. We, therefore, set out to determine whether NHE3 is necessary for Ca 2+ (re)absorption from these epithelia by comparing Ca 2+ handling between wild-type and NHE3 −/− mice. Serum Ca 2+ and plasma parathyroid hormone levels were not different between groups. However, NHE3 −/− mice had increased serum 1,25-dihydroxyvitamin D 3 . The fractional excretion of Ca 2+ was also elevated in NHE3 −/− mice. Paracellular Ca 2+ flux across confluent monolayers of a PT cell culture model was increased by an osmotic gradient equivalent to that generated by NHE3 across the PT in vivo and by overexpression of NHE3. 45 Ca 2+ uptake after oral gavage and flux studies in Ussing chambers across duodenum of wild-type and NHE3 −/− mice confirmed decreased Ca 2+ absorption in NHE3 −/− mice compared with wild-type mice. Consistent with this, intestinal calbindin-D 9K , claudin-2, and claudin-15 mRNA expression was decreased. Microcomputed tomography analysis revealed a perturbation in bone mineralization. NHE3 −/− mice had both decreased cortical bone mineral density and trabecular bone mass. Our results demonstrate significant alterations of Ca 2+ homeostasis in NHE3 −/− mice and provide a molecular link between Na + and Ca 2+ (re)absorption.
The Effect of Congestion Control Model on Congested Traffic Flow in Vehicular Ad Hoc Networks (VANETs)

Field: Computer Science (Physical Sciences)

This study seeks to conduct analytical investigation into Congestion Control models to determine the effects of parameters inherent in mitigating traffic flow density in a congested network. The spatial temporal variations in the value of λ affects vehicular traffic flow. This study proposed a Congestion Control Model and perform simulation in MATLAB. In this model, vehicular density and number of vehicles were held constant while varying the value of λ from 1 to 10. The simulation result reveals the vehicle trajectories as the value of λ increases with time. The outcome of this study indicates that there is no need increasing the value of λ beyond 12, since further increases would only increase the number of vehicles leading to traffic jam. In principle, it is very important to use 1≤ λ ≤12 in designing traffic models in VANETs. The analytical result proved that the Congestion Control Model for the four-lane may be the most appropriate model to be adopted and use in designing VANETs networks.
Independent Measurement of Ampicillin and Cloxacillin in Mixtures

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

A simplified method of assaying mixtures of ampicillin and cloxacillin is presented. The method consists of cylinder-plate assays of appropriately diluted samples in three assay systems in which: (i) cloxacillin is measured, utilizing agar seeded with a penicillinase-producing Staphylococcus aureus ; (ii) ampicillin is measured after the greatest dilution practicable, by use of agar seeded with Sarcina lutea ; and (iii) the proportion of activity found in the second assay that remains after treatment with staphylococcal penicillinase is determined on agar seeded with S. lutea . The error was 4% or less when each system was run in quadruplicate, except when there was 10 or more times as much cloxacillin as ampicillin, in which case the greatest error was 12%. Mixtures of methicillin with benzylpenicillin or with ampicillin can also be quantitated by this method.
The European Commission’s 2011 Progress Report on Turkey: more than just a hollow ritual?

Field: Social Sciences (Social Sciences)

The European Commission has released its 2011 Report on Turkey’s progress towards EU accession. Unfortunately, this is no more than following a ritual, a hollow gesture, since ‘progress’ is not that visible, especially considering that no new chapters have been opened following the Spanish Presidency in 2010. The European Commission’s annual report on Turkey’s progress towards EU accession was released on 12 October, a further episode in a ritual that began with a Regular Report in 1998. Prepared by the Directorate-General of Enlargement’s Turkey team, the report lays out the progress achieved during the year in political criteria, fundamental rights and freedoms and the economy. In addition, it provides an annual overview of developments in each negotiation chapter, one by one. This year’s report underlines issues related to the freedom of expression and of the press, which is an increasing concern in the country. Furthermore, the application of the rule of law is another hot topic as regards developments in the ongoing cases on alleged criminal networks, while regional and minority issues are always on the table when talking about Turkey.