Miracle-dz/UniFAR-FTUs huggingface dataset:
Online Paging with a Vanishing Regret

This paper considers a variant of the online paging problem, where the online algorithm has access to multiple predictors, each producing a sequence of predictions for the page arrival times. The predictors may have occasional prediction errors and it is assumed that at least one of them makes a sublinear number of prediction errors in total. Our main result states that this assumption suffices for the design of a randomized online algorithm whose time-average regret with respect to the optimal offline algorithm tends to zero as the time tends to infinity. This holds (with different regret bounds) for both the full information access model, where in each round, the online algorithm gets the predictions of all predictors, and the bandit access model, where in each round, the online algorithm queries a single predictor. While online algorithms that exploit inaccurate predictions have been a topic of growing interest in the last few years, to the best of our knowledge, this is the first paper that studies this topic in the context of multiple predictors. Moreover, to the best of our knowledge, this is also the first paper that aims for (and achieves) online algorithms with a vanishing regret for a classic online problem under reasonable assumptions.
Computational performance and accuracy of Sentieon DNASeq variant calling workflow

As reliable, efficient genome sequencing becomes more ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important. The Genome Analysis Toolkit (GATK), maintained by the Broad Institute, is currently the widely accepted standard for variant calling software. However, alternative solutions may provide faster variant calling without sacrificing accuracy. One such alternative is Sentieon DNASeq, a toolkit analogous to GATK but built on a highly optimized backend. We evaluated the DNASeq single-sample variant calling pipeline in comparison to that of GATK. Our results confirm the near-identical accuracy of the two software packages, showcase perfect scalability and great speed from Sentieon, and describe computational performance considerations for the deployment of Sentieon DNASeq.
Using Unity to Help Solve Intelligence

In the pursuit of artificial general intelligence, our most significant measurement of progress is an agent's ability to achieve goals in a wide range of environments. Existing platforms for constructing such environments are typically constrained by the technologies they are founded on, and are therefore only able to provide a subset of scenarios necessary to evaluate progress. To overcome these shortcomings, we present our use of Unity, a widely recognized and comprehensive game engine, to create more diverse, complex, virtual simulations. We describe the concepts and components developed to simplify the authoring of these environments, intended for use predominantly in the field of reinforcement learning. We also introduce a practical approach to packaging and re-distributing environments in a way that attempts to improve the robustness and reproducibility of experiment results. To illustrate the versatility of our use of Unity compared to other solutions, we highlight environments already created using our approach from published papers. We hope that others can draw inspiration from how we adapted Unity to our needs, and anticipate increasingly varied and complex environments to emerge from our approach as familiarity grows.
Preventive efficacy evaluation of Urtica dioica on in vitro fertilization and embryo development in exposed mice

Nowadays impact of cell-phone RF on human health is subject of many researches. Antioxidant properties of hydroalcoholic extract of Urtica dioica (UD) have been proven to eliminate free radicals and oxidative stress. Purpose of this study was to assess the impacts of cell-phone RF on in-vitro fertility (IVF) rate and role of the UD extract against induced the RF damages. A total number of 54 adult, male NMRI mice were randomly divided into six equal groups randomly; control group, RF-irradiation alone (2hrs a day for 28days), those received only 50mg/kg UD, 50mg/kg UD plus RF-irradiation, only 100mg/kg UD, and 100mg/kg UD plus RFirradiation. The UD was intraperitoneally injected 1hr before RF-irradiation. IVF performed 1day after the last RF-irradiation. Chromatin integrity in sperm DNA evaluated by acridine orange staining. Finally, frequency and morphology of the embryos were assessed. ANOVA and Tukey's tests applied for statistical analysis. RF-irradiation alone significantly decreased frequency of two-cell embryos (p=0.000) and grade-A embryos (p=0.014); while it significantly increased the dead embryos (p=0.001) and grade-B (p=0.033), grade-C (p=0.017) and grade-D embryos (p=0.008). RF-irradiation alone led to significant genetically damages in DNA chromatin (p=0.000). Injection of 100mg/kg UD increased significantly frequency of the two-cell embryos (p=0.01) and grade-A embryos (p=0.018); where it significantly reduced the dead embryos (p=0.026), grade-C (p=0.026) and grade-D embryos (p= 0.038). Cell-phone RF can change number of two-cell mouse embryo as well as embryo's morphology and induces molecular damages in the DNA of the sperm. Moreover, UD extract plays a protective role against RF induced damages.
On the Probability That a Rocky Planet’s Composition Reflects Its Host Star

The bulk density of a planet, as measured by mass and radius, is a result of planet structure and composition. Relative proportions of iron core, rocky mantle, and gaseous envelopes are degenerate for a given density. This degeneracy is reduced for rocky planets without significant gaseous envelopes when the structure is assumed to be a differentiated iron core and rocky mantle, in which the core mass fraction (CMF) is a first-order description of a planet’s bulk composition. A rocky planet’s CMF may be derived both from bulk density and by assuming the planet reflects the host star’s major rock-building elemental abundances (Fe, Mg, and Si). Contrasting CMF measures, therefore, shed light on the outcome diversity of planet formation from processes including mantle stripping, out-gassing, and/or late-stage volatile delivery. We present a statistically rigorous analysis of the consistency of these two CMF measures accounting for observational uncertainties of planet mass and radius and host-star chemical abundances. We find that these two measures are unlikely to be resolvable as statistically different unless the bulk density CMF is at least 40% greater than or 50% less than the CMF as inferred from the host star. Applied to 11 probable rocky exoplanets, Kepler-107 c has a CMF as inferred from bulk density that is significantly greater than the inferred CMF from its host star (2σ) and is therefore likely an iron-enriched super-Mercury. K2-229b, previously described as a super-Mercury, however, does not meet the threshold for a super-Mercury at a 1σ or 2σ level.
Your "Labrador" is My "Dog": Fine-Grained, or Not

Whether what you see in Figure 1 is a "labrador" or a "dog", is the question we ask in this paper. While fine-grained visual classification (FGVC) strives to arrive at the former, for the majority of us non-experts just "dog" would probably suffice. The real question is therefore -- how can we tailor for different fine-grained definitions under divergent levels of expertise. For that, we re-envisage the traditional setting of FGVC, from single-label classification, to that of top-down traversal of a pre-defined coarse-to-fine label hierarchy -- so that our answer becomes "dog"-->"gun dog"-->"retriever"-->"labrador". To approach this new problem, we first conduct a comprehensive human study where we confirm that most participants prefer multi-granularity labels, regardless whether they consider themselves experts. We then discover the key intuition that: coarse-level label prediction exacerbates fine-grained feature learning, yet fine-level feature betters the learning of coarse-level classifier. This discovery enables us to design a very simple albeit surprisingly effective solution to our new problem, where we (i) leverage level-specific classification heads to disentangle coarse-level features with fine-grained ones, and (ii) allow finer-grained features to participate in coarser-grained label predictions, which in turn helps with better disentanglement. Experiments show that our method achieves superior performance in the new FGVC setting, and performs better than state-of-the-art on traditional single-label FGVC problem as well. Thanks to its simplicity, our method can be easily implemented on top of any existing FGVC frameworks and is parameter-free.
DISEASES OF BILIARY SYSTEM AND DIABETES MELLITUS TYPE II: ACCIDENTAL OR EXPECTED COMORBIDITY

DISEASES OF BILIARY SYSTEM AND DIABETES MELLITUS TYPE II: ACCIDENTAL OR EXPECTED COMORBIDITYZhuravlyova L.V. , Tymoshenko G.Yu. Kharkiv National Medical University, UkraineAbstract. The issues of comorbid abnormalities secondary to diabetes mellitus (DM) become more relevant year by year and attract the attention of many researchers and clinicians due to a steady increase in the incidence and development of complications. The etiology and pathogenesis of dysfunctional diseases of the biliary system and diabetes mellitus type II (DM-2) are not fully understood up to this day. Understanding etiopathogenetical mechanisms and relationship of these diseases will help to improve their diagnostics and will increase the effectiveness of medical interventions resulting in enhancing of disease prognosis and quality of life.Key words: diabetes mellitus type II, biliary system diseases, chronic cholecystitis, bile acids. Захворювання біліарної системи та цукровий діабет 2 типу: випадкова чи закономірна коморбідністьЖуравльова Л. В. , Тимошенко Г. Ю. Харківський національний медичний університет, УкраїнаРезюме. Проблеми коморбідної патології на тлі цукрового діабету (ЦД) з кожним роком стають більш актуальними та привертають увагу багатьох науковців та клініцистів, у зв’язку з неухильним ростом захворюваності та розвитком ускладнень. До теперішнього часу етіологія та патогенез дисфункціональних захворювань біліарної системи та цукрового діабету 2 типу (ЦД-2) залишаються не до кінця вивченими. Розуміння етіопатогенетичних механізмів та взаємозв’язків цих захворювань сприятимуть удосконаленню їх діагностики та дозволить підвищити ефективність лікувальних заходів, що призведе до покращання прогнозу захворювань та якості життя. Ключові слова: цукровий діабет 2 типу, захворювання біліарної системи, хронічний холецистит, жовчні кислоти. Заболевания билиарной системы и сахарный диабет 2 типа: случайная или закономерная коморбидностьЖуравлева Л. В. , Тимошенко Г. Ю. Харьковский национальный медицинский университет, УкраинаРезюме. Проблемы коморбидной патологии на фоне сахарного диабета (СД) с каждым годом становятся более актуальными и привлекают внимание многих ученых и клиницистов, в связи с неуклонным ростом заболеваемости и развитием осложнений. К настоящему времени этиология и патогенез дисфункциональных заболеваний билиарной системы и сахарного диабета 2 типа (СД-2) остаются не до конца изученными. Понимание этиопатогенетических механизмов и взаимосвязей этих заболеваний будут способствовать усовершенствованию их диагностики и позволит повысить эффективность лечебных мероприятий, что приведет к улучшению прогноза заболеваний и качества жизни. Ключевые слова: сахарный диабет 2 типа, заболевания билиарной системы, хронический холецистит, желчные кислоты.
OMA standalone: orthology inference among public and custom genomes and transcriptomes

Genomes and transcriptomes are now typically sequenced by individual labs, but analysing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this is far from trivial. The OMA (Orthologous MAtrix) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and pre-computed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of the Lophotrochozoa, a challenging clade within the Protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in non-model organisms. OMA Standalone is available at http://omabrowser.org/standalone under the permissible open source Mozilla Public License Version 2.0.
Infrared and Raman Spectroscopy: Principles and Spectral Interpretation

"Infrared and Raman Spectroscopy: Principles and Spectral Interpretation" explains the background, core principles and tests the readers understanding of the important techniques of Infrared and Raman Spectroscopy. These techniques are used by chemists, environmental scientists, forensic scientists etc to identify unknown chemicals. In the case of an organic chemist these tools are part of an armory of techniques that enable them to conclusively prove what compound they have made, which is essential for those being used in medical applications. The book reviews basic principles, instrumentation, sampling methods, quantitative analysis, origin of group frequencies and qualitative interpretation using generalized Infrared (IR) and Raman spectra. An extensive use of graphics is used to describe the basic principles of vibrational spectroscopy and the origins of group frequencies, with over 100 fully interpreted FT-IR and FT-Raman spectra included and indexed to the relevant qualitative interpretation chapter. A final chapter with forty four unknown spectra and with a corresponding answer key is included to test the readers understanding. Tables of frequencies (peaks) for both infrared and Raman spectra are provided at key points in the book and will act as a useful reference resource for those involve interpreting spectra. This book provides a solid introduction to vibrational spectroscopy with an emphasis placed upon developing critical interpretation skills. It is ideal for those using and analyzing IR and Raman spectra in their laboratories as well as those using the techniques in the field. It uniquely integrates discussion of IR and Raman spectra. Theory illustrated and explained with over 100 fully interpreted high quality FT-IR and FT-Raman spectra (4 cm-1 resolution). There are selected problems at the end of chapters and 44 unknown IR and Raman spectra to test readers understanding (with a corresponding answer key).
Crystal structures of intermetallic compounds

Contributors Preface to the 1995 Edition Preface to Reprint Volumes Acronyms Crystal Structure Nomenclature 1 Factors Governing Crystal Structures Pierre Villars 2 Close-Packed Structures Jurgen Hauck and Klaus Mika 3 Body-Centered Cubic Derivative Structures Erwin E. Hellner and Roland Schwarz 4 Wurtzite and Sphalerite Structures Erwin Parthe 5 Atomic Environments in Some Related Intermetallic Structure Types Jo L. C. Daams 6 Some Important Structures of Fixed Stoichiometry Michael V. Nevitt and Carl C. Koch 7 Topologically Close-Packed Structures Evgen I. Gladyshevskii and Oksana Bodak 8 Structure Mapping David G. Pettifor 9 Magnetic Structures Walter L. Roth 10 Quasicrystals and Related Structures Kenneth F. Kelton Index Contents of 1995 edition
The impact of connexins on atherogenesis: A brief review

Connexins family in humans consists of 21 highly conserved proteins that are responsible for contact formation between cells. On the cell surface, connexins form hemichannels, or connexons. Two hemichannels brought together form a gap junction, a form of intercellular contact that allows for direct transfer of material and signals between the adjacent cells. Gap junctions serve for transporting ions and other soluble, low molecular weight molecules therefore synchronizing the microenvironment of the contacting cells, and maintaining cell and tissue homeostasis. Impairment of gap junctions is associated with different pathological conditions. Importantly, it has been described in atherosclerosis, which causes local cellular dysfunction in the arterial wall tissues followed by the development of atherosclerotic plaque. There are 3 main connexins expressed in human cardiovascular system: Connexin 37 (Cx37), Cx40, and Cx43. Alterations in the arterial wall cells observed in atherosclerosis include changes in the expression pattern of the main connexins, and impairment of intercellular contacts and communication. According to the currently available data, Cx37 and Cx40 have anti-atherogenic and vasculoprotective properties, while Cx43 appears to be more pro-atherogenic. However, the effects of connexins are cell type-dependent and in many cases, remain to be studied in detail. In this review, we summarize the available knowledge on connexins of the arterial wall cells involved in atherosclerosis development.
Endothelial Protection by High-Density Lipoproteins

There are several potential mechanisms by which HDLs protect against the development of vascular disease. One relates to the unique ability of these lipoproteins to remove cholesterol from the arterial wall. Another is the ability of HDL to prevent and eventually correct endothelial dysfunction, a key variable in the pathogenesis of atherosclerosis and its complications. HDLs help maintain endothelial integrity, facilitate vascular relaxation, inhibit blood cell adhesion to vascular endothelium, reduce platelet aggregability and coagulation, and may favor fibrinolysis. These functions of HDLs complement their activity in arterial cholesterol removal by providing an excellent rationale for favorably influencing pathological processes underlying a variety of clinical conditions, such as accelerated atherosclerosis, acute coronary syndromes, and restenosis after coronary angioplasty, through a chronic or acute elevation of plasma HDL concentration.
Vertical variability of Euphausia distinguenda metabolic rates during diel migration into the oxygen minimum zone of the Eastern Tropical Pacific off Mexico

 INSTITUTO DE OCEANOGRAFÍA Y CAMBIO GLOBAL, IOCAG, UNIVERSIDAD DE LAS PALMAS DE GRAN CANARIA, ULPGC, UNIDAD ASOCIADA ULPGC‐CSIC, LAS PALMAS DE GRAN CANARIA, SPAIN, INSTITUTO ESPAÑOL DE OCEANOGRAFÍA, CENTRO OCEANOGRÁFICO DE MÁLAGA, PUERTO PESQUERO S/N, , FUENGIROLA, MÁLAGA, SPAIN, INTER-AMERICAN TROPICAL TUNA COMMISSION, LA JOLLA, CA, USA, UNIVERSIDAD DEL VALLE, DEPARTAMENTO DE BIOLOGÍA. GRUPO DE INVESTIGACIÓN EN ECOLOGÍA ANIMAL, A.A. , CALI, COLOMBIA AND CENTRO DE INVESTIGACIÓN CIENTÍFICA Y DE EDUCACIÓN SUPERIOR DE ENSENADA. DIVISIÓN DE OCEANOLOGÍA. DEPARTAMENTO DE ECOLOGÍA. ENSENADA, MÉXICO
96 dB Linear High Dynamic Range CAOS Spectrometer Demonstration

For the first time, a CAOS (i.e., Coded Access Optical Sensor) spectrometer is demonstrated. The design implemented uses a reflective diffraction grating and a time-frequency CAOS mode operations Digital Micromirror Device (DMD) in combination with a large area point photo-detector to enable highly programmable linear High Dynamic Range (HDR) spectrometry. Experiments are conducted with a 2850 K color temperature light bulb source and visible band color bandpass and high-pass filters as well as neutral density (ND) attenuation filters. A ~369 nm to ~715 nm input light source spectrum is measured with a designed ~1 nm spectral resolution. Using the optical filters and different CAOS modes, namely, Code Division Multiple Access (CDMA), Frequency Modulation (FM)-CDMA and FM-Time Division Multiple Access (TDMA) modes, measured are improving spectrometer linear dynamic ranges of 28 dB, 50 dB, and 96.2 dB, respectively. Applications for the linear HDR CAOS spectrometer includes materials inspection in biomedicine, foods, forensics, and pharmaceuticals.
Molecular and morphological evidence for three sympatric species of Leptanilla (Hymenoptera: Formicidae) on the Greek island of Rhodes

Ants of the genus Leptanilla have a broad distribution in the Paleotropical and southern Palearctic regions. Workers are eyeless, strictly subterranean and rarely encountered, whereas the males possess eyes and fully developed wings, and are collected with greater frequency in pan traps, in Malaise traps, and at lights. As a result of these circumstances a parallel taxonomy has developed for workers and males, with little or no attempt at integration of the two systems. Molecular markers have the potential to link the two sexes and permit reconciliation of the two taxonomies. Here we analyze a sample of fourteen Leptanilla males from a single site on the island of Rhodes, Greece, using morphology and DNA sequence data (ten nuclear genes; 8.6 kb of aligned sequence data). The two sources of data are fully concordant, and indicate the occurrence of three sympatric species. Phylogenetic relationships of these taxa and two other Leptanilla species are estimated using Bayesian inference and maximum likelihood. Two of the species, Leptanilla GR01 and Leptanilla GR03 are sister taxa in these analyses, while Leptanilla GR02 is more distantly related. Within this sample we observe almost no intraspecific genetic or morphological variation, but there are substantial differences among the species. The divergent DNA sequences provide an opportunity to identify the corresponding workers of these Leptanilla species.
Effects of narrow-band ultraviolet B on the expression of keratin 17 in keratinocytes

Objective To investigate the effects of narrow-band ultraviolet B (NB-UVB) on the expression of keratin 17 (K17) in the human keratinocyte cell line HaCaT.Methods Cultured HaCaT cells were irradiated with different doses (0,50,100,200,400 mJ/cm2) of NB-UVB followed by additional culture for 6,12 and 24 hours respectively.To explore the mechanisms underlying the effects of NB-UVB on K17 expression,some HaCaT cells were pretreated with PD98059 (an inhibitor of mitogen-activated protein kinase kinase) followed by UVB radiation and additional culture as described above.Cell counting kit-8 (CCK 8) was used to evaluate the proliferation of,real time PCR to measure the mRNA expressions of K17 in,and Western blot to determine the protein expression of K17,Erk1/2 and phosphorylated Erk1/2 in,HaCaT ceils.Results Both the proliferation of and K17 expression in HaCaT cells were promoted by NB-UVB radiation at low doses (50,100 mJ/cm2),but inhibited by NB-UVB radiation at high doses (200,400 mJ/cm2). Significant differences were observed for the proliferative activity between HaCaT cells irradiated with NB-UVB at 100 or 400 mJ/cm2 and unirradiated HaCaT ceils at 12 and 24 hours (P ＜ 0.01 or 0.05). The phosphorylation of Erk1/2 was upregulated by NB-UVB radiation at 100 mJ/cm2,but downregulated by that at 400 mJ/cm2,and the upregulation induced by low dose NB-UVB could be suppressed by blocking the Erk 1/2 pathway.Conclusion The effects of NB-UVB radiation on K17 expression may be modulated by the Erk 1/2 pathway. Key words: Ultraviolet rays; Keratinocytes; Keratin-17; Cell proliferation; Phosphorylases