Miracle-dz/UniFAR-FTUs huggingface dataset:
Ab initio simulations of Cu binding sites in the N-terminal region of PrPs

The prion protein (PrP) binds Cu2+ ions in the octarepeat domain of the N-terminal tail up to full occupancy at pH=7.4. Recent experiments show that the HGGG octarepeat subdomain is responsible for holding the metal bound in a square planar coordination. By using first principle ab initio molecular dynamics simulations of the Car-Parrinello type, the Cu coordination mode to the binding sites of the PrP octarepeat region is investigated. Simulations are carried out for a number of structured binding sites. Results for the complexes Cu(HGGGW)+(wat), Cu(HGGG) and the dimer [Cu(HGGG)]2 are presented. While the presence of a Trp residue and a H2O molecule does not seem to affect the nature of the Cu coordination, high stability of the bond between Cu and the amide Nitrogens of deprotonated Gly’s is confirmed in the case of the Cu(HGGG) system. For the more interesting [Cu(HGGG)]2 dimer a dynamically entangled arrangement of the two monomers, with intertwined N-Cu bonds, emerges. This observation is consistent with the highly packed structure seen in experiments at full Cu occupancy.
Exploring the association between alcohol, marijuana, and secondhand effects with rural college students

ABSTRACT The current study investigated the association between secondhand effects and personal consequences with substance use in a sample of rural college students (N = 412; 55.1% women; 92.2% white/non-Hispanic). The study extends the body of secondhand effects research by (a) investigating the association of marijuana use with the experience of secondhand effects; (b) examining the association of onset risk of substance use (< 18 years old) with the experience of secondhand effects; (c) exploring the multiplicity of experienced effects associated with substance use by employing a four-category typology that exhaustively represents exposure to secondhand effects and personal consequences. Bivariate and multiple regression analyses were used to evaluate the data. The majority of students (90.3%) experienced undesirable effects from substance use, with 15% reporting only secondhand effects, 28.5% only personal consequences, and 46.8% reporting both secondhand effects and personal consequences. Residing on-campus, onset risk, and past 30-day alcohol or marijuana use increased risk for experiencing personal consequences and the combination of secondhand effects and personal consequences. Secondhand effects are likely to compound the harm for substance users because they often experience both secondhand effects and personal consequences.
The Mathematics of Non-Individuality

Some of the forerunners of quantum theory regarded the basic entities of such theories as 'non-individuals'. One of the problems is to treat collections of such 'things', for they do not obey the axioms of standard set theories like Zermelo-Fraenkel. In this paper, collections of objects to which the standard concept of identity (Leibinizian identity) does not apply are termed 'quasi-sets'. The motivation for such a theory, linked to what we call 'the Manin problem', is presented, so as its specific axioms. At the end, it is shown how quantum statistics can be obtained within quasi-set thbeory.
Increasing Trend of Colorectal Cancer Incidence in Korea, 1999-2009

Purpose This study was conducted in order to demonstrate changing trends in colorectal cancer incidence according to sex, age group, and anatomical location in the Korean population. Materials and Methods Data from the Korea Central Cancer Registry between 1999 and 2009 were analyzed. Annual percent changes (APCs) of sex- and age-specific incidence rates for cancer of the proximal colon (International Statistical Classification of Diseases and Related Health Problems, 10th revision [ICD-10] code C18.0-18.5), distal colon (C18.6-18.7), and rectum (C19-20), and male-to-female incidence rate ratios (IRR) were calculated. Results The age-standardized incidence rate (ASR) of colorectal cancer was 27 (per 100,000) in 1999 and increased to 50.2 in 2009 among men (APC, 6.6%). The ASR for women was 17.2 in 1999 and 26.9 in 2009 (APC, 5.1%). The rectum was the most common site of cancer among both men and women during 1999 and 2009. However, the distal colon had the highest APC (10.8% among men and 8.4% among women), followed by the proximal colon (7.9% among men and 6.6% among women), and rectum (5.2% among men and 2.4% among women). The proportion of rectal cancer decreased from 51.5% in 1999 to 47.1% in 2009 among men, and from 50.5% to 42.8% among women. An increase in the male-to-female IRR was observed for distal colon cancer and rectal cancer, whereas the IRR for proximal colon cancer was stable. Conclusion The rapid increase in colorectal cancer incidence is mainly attributed to the increase in colon cancer, especially distal colon cancer, and may be explained by a transition of risk factors for subsites or by the effect of colorectal cancer screening.
Khat Dependency and Psychophysical Symptoms among Chewers in Jazan Region, Kingdom of Saudi Arabia

Background. Khat chewing is highly prevalent in Africa, Yemen and Jazan region, southwest of Saudi Arabia. Most of Jazani Khat chewers consider khat session as a social activity and do not consider khat dependency. The aim of this study was to explore khat dependency and its relationship with the psychophysical symptoms among chewers. Methods. Cross-sectional study on seventy Saudi male khat chewers living in Jazan area. Psychological dependence to khat chewing was evaluated using the Severity of Dependency Scale (SDS). The participants filled in a self-administrated assisted structured questionnaire designed to collect data about their medical history, neurological symptoms, and their chewing behavior. Results. Half (52.2%) of khat chewers showed psychological dependency. Those having longer khat sessions (≥6 hours) were more liable for dependency. Physical and psychological symptoms were more prevalent among khat dependent chewers. Conclusions. khat has a psychological dependence effect that can be measured by the SDS, even in low doses and with irregular use. SDS scale is a useful tool to expect the burden of either physical or psychological symptoms on khat chewers.
A Stretched Exponential Law for the Average Time History of Gamma-Ray Bursts and Their Time Dilations

Individual gamma-ray bursts (GRBs) have very diverse time behavior—from a single pulse to a long complex sequence of chaotic pulses of different timescales. I studied time profiles of GRBs using data from the Compton Gamma Ray Observatory's Burst and Transient Source Experiment (BATSE) and found that the postpeak slope of the average peak-aligned time profile of GRBs obeys a unique and simple analytical law, I ~ exp [-(t/t0)1/3], where t is the time measured from the peak of the event and t0 is a constant ranging from 0.3 s for strong bursts to ~1 s for weak bursts. The average peak-aligned time profile follows this law with good accuracy in the whole time range available for analysis (from fractions of a second to ~120 s after the peak). Such a law (a stretched exponential) appears in processes associated with fractals (e.g., turbulence). The same analysis for solar flares gives a different shape for the average time profile. The dependence of t0 on the brightness of GRBs is presented. The time dilation of the dimmest GRBs relative to the brightest GRBs is at least a factor ~2 and possibly ~3. The statistics (600 GRBs), however, still does not allow us to rule out an intrinsic anticorrelation between intensity and duration of GRBs as a possible explanation of the effect. Probably, it is possible to confirm (or disprove) the cosmological origin of GRBs using the total existing statistics of strong bursts.
Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress

Acidovorax avenae subsp. avenae is the causal agent of bacterial brown stripe disease in rice. In this study, we characterized a novel horizontal transfer of a gene cluster, including tetR, on the chromosome of A. avenae subsp. avenae RS-1 by genome-wide analysis. TetR acted as a repressor in this gene cluster and the oxidative stress resistance was enhanced in tetR-deletion mutant strain. Electrophoretic mobility shift assay demonstrated that TetR regulator bound directly to the promoter of this gene cluster. Consistently, the results of quantitative real-time PCR also showed alterations in expression of associated genes. Moreover, the proteins affected by TetR under oxidative stress were revealed by comparing proteomic profiles of wild-type and mutant strains via 1D SDS-PAGE and LC-MS/MS analyses. Taken together, our results demonstrated that tetR gene in this novel gene cluster contributed to cell survival under oxidative stress, and TetR protein played an important regulatory role in growth kinetics, biofilm-forming capability, superoxide dismutase and catalase activity, and oxide detoxicating ability.
Disentangling Complexity from Randomness and Chaos

This study aims to disentangle complexity from randomness and chaos, and to present a definition of complexity that emphasizes its epistemically distinct qualities. I will review existing attempts at defining complexity and argue that these suffer from two major faults: a tendency to neglect the underlying dynamics and to focus exclusively on the phenomenology of complex systems; and linguistic imprecisions in describing these phenomenologies. I will argue that the tendency to discuss phenomenology removed from the underlying dynamics is the main root of the difficulties in distinguishing complex from chaotic or random systems. In my own definition, I will explicitly try to avoid these pitfalls. The theoretical contemplations in this paper will be tested on a sample of five models: the random Kac ring, the chaotic CA30, the regular CA90, the complex CA110 and the complex Bak-Sneppen model. Although these modelling studies are restricted in scope and can only be seen as preliminary, they still constitute on of the first attempts to investigate complex systems comparatively.
Epidural Steroids: A Comprehensive, Evidence-Based Review

Abstract Epidural steroid injections (ESIs) are the most widely utilized pain management procedure in the world, their use supported by more than 45 placebo-controlled studies and dozens of systematic reviews. Despite the extensive literature on the subject, there continues to be considerable controversy surrounding their safety and efficacy. The results of clinical trials and review articles are heavily influenced by specialty, with those done by interventional pain physicians more likely to yield positive findings. Overall, more than half of controlled studies have demonstrated positive findings, suggesting a modest effect size lasting less than 3 months in well-selected individuals. Transforaminal injections are more likely to yield positive results than interlaminar or caudal injections, and subgroup analyses indicate a slightly greater likelihood for a positive response for lumbar herniated disk, compared with spinal stenosis or axial spinal pain. Other factors that may increase the likelihood of a positive outcome in clinical trials include the use of a nonepidural (eg, intramuscular) control group, higher volumes in the treatment group, and the use of depo-steroid. Serious complications are rare following ESIs, provided proper precautions are taken. Although there are no clinical trials comparing different numbers of injections, guidelines suggest that the number of injections should be tailored to individual response, rather than a set series. Most subgroup analyses of controlled studies show no difference in surgical rates between ESI and control patients; however, randomized studies conducted by spine surgeons, in surgically amenable patients with standardized operative criteria, indicate that in some patients the strategic use of ESI may prevent surgery.
La comprensión lectora y el rendimiento escolar

Este escrito pretende determinar las posibles relaciones entre el nivel de comprension lectora de los estudiantes y su desempeno academico. Se realiza un estudio descriptivo y un analisis estadistico correlacional. Se aplico el instrumento Prueba de Competencia Lectora para Educacion Secundaria (CompLEC) a estudiantes de ambos sexos con edades comprendidas entre los 13 y 14 anos del grado noveno de educacion basica de una institucion educativa publica. A partir del analisis descriptivo, los estudiantes presentan dificultades en el orden textual, inferencial y contextual; en el analisis correlacional de los datos de las diferentes asignaturas (Ciencias Naturales, Ciencias Sociales, Lengua Castellana y Matematicas) tienen una correlacion significativa positiva, pero no significa necesariamente la existencia de una relacion de causa-efecto.
The Experience of Movement Meditation: A Dance of Rhythmic Paradox and Time

There has been a growing interest in non-Western approaches to attention, consciousness, health, and healing. One largely unexplored tradition stems from the teachings of Gurdjieff, which focus on movement meditation. The purpose of this qualitative study was to explore the experience of movement meditation as a first step toward determining potential for health and healing. Phenomenology was selected to explore the experience of movement meditation. The essential structure of the experience of movement meditation reflected three elements: (a) an in-the-moment experience of movement meditation, (b) outcomes of movement meditation, and (c) metathemes that surround the whole experience of movement meditation.
Concerns of Teachers and Principals on Instructional Supervision in Three Asian Countries

This study discusses on the nature of instructional supervision carried out in schools in three Asian countries India, Malaysia and Thailand. This study followed the qualitative method involving questionnaire and interview. About hundred teachers and twenty five principals and other heads from three countries participated in this study. The questionnaire was sent trough post or email while interview was conducted either face to face or online using msn or Skype. The responding rate of participants was hundred percent. The discussion was focused on four themes that are related to the research questions namely supervision as a continuous, developmental and corporate process; supervision as a specialists' area, the role of principals and teachers in instructional supervision and benefits to the teachers through instructional supervision. Evidences of findings accounted for instructional supervision being just eye wash, a paper completion and punitive process and non beneficial to the teachers. The participants stressed for involving teachers, principals, subject teachers and subject specialist to make instructional supervision practices more meaningful. The findings advocated for supervision to be continuous development and corporate process.
Throughput-Delay Tradeoff for Hierarchical Cooperation in Ad Hoc Wireless Networks

Hierarchical cooperation has recently been shown to achieve better throughput scaling than classical multihop schemes under certain assumptions on the channel model in static wireless networks. However, the end-to-end delay of this scheme turns out to be significantly larger than those of multihop schemes. A modification of the scheme is proposed here that achieves a throughput-delay tradeoff <i>D</i>(<i>n</i>) = (log<i>n</i>)<sup>2</sup> <i>T</i>(<i>n</i>) for <i>T</i>(<i>n</i>) between <i>¿(¿(n)</i>/log<i>n</i>) and <i>¿(n</i>/log<i>n</i>), where <i>D</i>(<i>n</i>) and <i>T</i>(<i>n</i>) are respectively the average delay per bit and the aggregate throughput in a network of <i>n</i> nodes. This tradeoff complements the previous results of El Gamal et al. , which show that the throughput-delay tradeoff for multihop schemes is given by <i>D</i>(<i>n</i>) = <i>T</i>(<i>n</i>) where <i>T</i>(<i>n</i>) lies between <i>¿(1)</i> and <i>¿(¿(n</i>).
PENGARUH EFIKASI DIRI DAN KREATIVITAS TERHADAP INTENSI BERWIRAUSAHA PADA SISWA KELAS XI SMK NEGERI POGALAN TAHUN AJARAN 2017/2018

Penelitian ini bertujuan untuk mengetahui : 1) Pengaruh Efikasi Diri terhadap Intensi Berwirausaha, 2) Pengaruh Kreativitas terhadap Intensi Berwirausaha, 3) Pengaruh Efikasi Diri dan Kreativitas terhadap Intensi Berwirausaha. Metode penelitian ini merupakan penelitian kuantitatif. Populasi dalam penelitian ini siswa kelas XI yang berjumlah 281 siswa. Sampel penelitian adalah 69 siswa yang diambil dengan metode propotional random sampling. Variabel penelitian yaitu Efikasi Diri (X 1 ), Kreativitas (X 2 ), dan Intensi Berwirausaha (Y). Teknik pengumpulan data dengan menggunakan metode angket (kuisioner). Hasil analisis dalam penelitian ini menunjukkan : (1) Secara parsial nilai t hitung (2,217) > t tabel (1,996) dan tingkat signifikasi 0,030 t tabel (1,996) dan tingkat signifikasi 0,037 F tabel 3,14 dan tingkat signifikan 0,000 < 0,050, sehingga dapat ditarik kesimpulan bahwa ada pengaruh yang signifikan antara efikasi diri dan kreativitas terhadap intensi berwirausaha pada siswa kelas XI SMK Negeri 1 Pogalan tahun ajaran 2017/2018. Secara keseluruhan efikasi diri dan kreativitas terhadap intensi berwirausaha sebesar 23,4%, sedangkan sisanya sebesar 76,6% dipengaruhi oleh faktor lain diluar variabel dalam penelitian ini.
Formation of subtropical westerly jet core in an idealized GCM without mountains

In boreal winter, subtropical westerlies in the upper troposphere reach maxima in speed over the eastern edges of the Asian and North American continents. The zonal variations in the westerlies are generally attributed to large‐scale orography and thermal forcing, but the latter mechanism remains largely unsubstantiated. Here we conduct general circulation model (GCM) experiments without orography to identify the most important thermal forcing for generating zonal asymmetries in subtropical westerlies. By changing sea surface temperature (SST) distribution in the GCM, we find that the tropical SST distribution plays a decisive role in producing a subtropical jet core to the north of the tropical warm water pool, while the effects of extratropical continent‐ocean heating contrast on upper‐level zonal wind speed distribution are secondary. The results from Aqua Planet runs further support this conclusion.
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale comparative genomics projects, and more. The pVOGs database represents a comprehensive set of orthologous gene families shared across multiple complete genomes of viruses that infect bacterial or archaeal hosts (viruses of eukaryotes will be added at a future date). The pVOGs are constructed within the Clusters of Orthologous Groups (COGs) framework that is widely used for orthology identification in prokaryotes. Since the previous release of the POGs, the size has tripled to nearly 3000 genomes and 300 000 proteins, and the number of conserved orthologous groups doubled to 9518. User-friendly webpages are available, including multiple sequence alignments and HMM profiles for each VOG. These changes provide major improvements to the pVOGs database, at a time of rapid advances in virus genomics. The pVOGs database is hosted jointly at the University of Iowa at http://dmk-brain.ecn. uiowa.edu/pVOGs and the NCBI at ftp://ftp.ncbi. nlm.nih. gov/pub/kristensen/pVOGs/home.html.
An efficient hybrid synchronization technique for scalable multi-core instruction set simulations

Multi-core system simulation techniques have been especially essential to system development in recent years. Although these techniques have been studied extensively, we have found that both conventional polling and collaborative timing synchronization approaches all encounter a severe scalability issue when the number of target cores is more than that of the host cores. To resolve this issue, we propose an effective hybrid technique that combines the advantage of the two approaches. According to the experimental results, the proposed technique effectively resolves the scalability issue and shows one to four orders of improvement compared to conventional approaches.
Random Walk with Restart on Large Graphs Using Block Elimination

Given a large graph, how can we calculate the relevance between nodes fast and accurately? Random walk with restart (RWR) provides a good measure for this purpose and has been applied to diverse data mining applications including ranking, community detection, link prediction, and anomaly detection. Since calculating RWR from scratch takes a long time, various preprocessing methods, most of which are related to inverting adjacency matrices, have been proposed to speed up the calculation. However, these methods do not scale to large graphs because they usually produce large dense matrices that do not fit into memory. In addition, the existing methods are inappropriate when graphs dynamically change because the expensive preprocessing task needs to be computed repeatedly. In this article, we propose Bear, a fast, scalable, and accurate method for computing RWR on large graphs. Bear has two versions: a preprocessing method BearS for static graphs and an incremental update method BearD for dynamic graphs. BearS consists of the preprocessing step and the query step. In the preprocessing step, BearS reorders the adjacency matrix of a given graph so that it contains a large and easy-to-invert submatrix, and precomputes several matrices including the Schur complement of the submatrix. In the query step, BearS quickly computes the RWR scores for a given query node using a block elimination approach with the matrices computed in the preprocessing step. For dynamic graphs, BearD efficiently updates the changed parts in the preprocessed matrices of BearS based on the observation that only small parts of the preprocessed matrices change when few edges are inserted or deleted. Through extensive experiments, we show that BearS significantly outperforms other state-of-the-art methods in terms of preprocessing and query speed, space efficiency, and accuracy. We also show that BearD quickly updates the preprocessed matrices and immediately computes queries when the graph changes.
The "parity" anomaly on an unorientable manifold

The “parity” anomaly—more accurately described as an anomaly in time-reversal or reflection symmetry—arises in certain theories of fermions coupled to gauge fields and/or gravity in a spacetime of odd dimension. This anomaly has traditionally been studied on orientable manifolds only, but recent developments involving topological superconductors have made it clear that one can get more information by asking what happens on an unorientable manifold. In this paper, we give a full description of the “parity” anomaly for fermions coupled to gauge fields and gravity in 2+1 dimensions on a possibly unorientable spacetime. We consider an application to topological superconductors and another application to M theory. The application to topological superconductors involves using knowledge of the “parity” anomaly as an ingredient in constructing gapped boundary states of these systems and in particular in gapping the boundary of a ν=16 system in a topologically trivial fashion. The application to M theory involves showing the consistency of the path integral of an M theory membrane on a possibly unorientable worldvolume. In the past, this has been done only in the orientable case.