Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosomal Analysis: Clinical Applicability to Brain Cancers

Cytogenetics is the branch of genetics that studies the cell activity focusing mainly on the chromosome structure, organization and function, isolated or as the whole karyotype, in order to understand aspects of cell biology, evolution or implicated diseases. The behavior of DNA and genes is greatly constrained by the fact that they are incorporated into chromosomes. The DNA is associated with proteins that control and catalyze the processes of transcription and replication. Gene expression is controlled by modifications in histones and by chromatin remodeling complexes. It can also be influenced by the position of the gene in the chromosome. Hence, errors in chromosome behavior are an important cause of ill-health. The presence of chromosomal abnormalities is usual in cancer, and specific chromosome abnormality may often be one of the first events in the development of cancer [1]. The importance of cytogenetic analysis in oncology is demonstrated by the number of researches made on this area since the discovery of the Philadelphia chromosome, a 9/22 translocation, which is seen in chronic myelogenous leukemia (CML) patients [2]. The focus of these studies is the relation between specific chromosome alterations to prognosis, drug resistance and diagnosis for some tumors entities. Moreover, DNA repair problems and others genomic stability pathways defects may lead to genome-wide genetic instability, which can drive further cancer progression [3]. Although chromosome rearrangements are mainly used as markers in hematologic cancers, these alterations have been increasingly studied in solid tumors (90% of all human malignan‐ cies), showing that chromosomal numerical/structural aberrations are common in this kind of neoplasia.
Multi-modal visual concept classification of images via Markov random walk over tags

Automatic annotation of images is a challenging task in computer vision because of “semantic gap” between highlevel visual concepts and image appearances. Therefore, user tags attached to images can provide further information to bridge the gap, even though they are partially uninformative and misleading. In this work, we investigate multi-modal visual concept classification based on visual features and user tags via kernel-based classifiers. An issue here is how to construct kernels between sets of tags. We deploy Markov random walks on graphs of key tags to incorporate co-occurrence between them. This procedure acts as a smoothing of tag based features. Our experimental result on the ImageCLEF2010 PhotoAnnotation benchmark shows that our proposed method outperforms the baseline relying solely on visual information and a recently published state-of-the-art approach.
Using the web to look for work: Implications for online job seeking and recruiting

Purpose – The web is now a significant component of the recruitment and job search process. However, very little is known about how companies and job seekers use the web, and the ultimate effectiveness of this process. The specific research questions guiding this study are: how do people search for job‐related information on the web? How effective are these searches? And how likely are job seekers to find an appropriate job posting or application? Design/methodology/approach – The data used to examine these questions come from job seekers submitting job‐related queries to a major web search engine at three points in time over a five‐year period.Findings – Results indicate that individuals seeking job information generally submit only one query with several terms and over 45 percent of job‐seeking queries contain a specific location reference. Of the documents retrieved, findings suggest that only 52 percent are relevant and only 40 percent of job‐specific searches retrieve job postings.Research limitations.
Culture of Yeast for the Production of Heterologous Proteins

This unit describes culture of the yeast strains Saccharomyces cerevisiae and Pichia pastoris for the production of foreign proteins. The protocols listed here for S. cerevisiae are for three widely used types of promoter: galactose‐regulated (GAL1, GAL7, GAL10), glucose‐repressible (e.g., ADH2), and constitutive glycolytic (e.g., PGK or GAPDH). Minor variations to each can be made depending on the selection system used. The P. pastoris expression system uses integrating vectors with the methanol‐regulated AOX1 promoter and HIS4 selection marker; although transformants are stable, they are generally grown in minimal selective medium. Methods are described for small‐scale S. cerevisiae and P. pastoris cultures and also for high‐density fermentations with these yeasts. A simple feeding strategy based on calculated feed rates is provided for S. cerevisiae and yields cell densities of 10 to 30 g/liter. In contrast, with P. pastoris, basic fermenter equipment is used to obtain extremely high‐density cultures (e.g., 130 g/liter). Finally, a describes small‐scale preparation of protein extracts.
Serum IL-17A in Newly Diagnosed Treatment-Naive Patients with Ulcerative Colitis Reflects Clinical Disease Severity and Predicts the Course of Disease

Background:The clinical course of ulcerative colitis (UC) is unpredictable. The need for reliable biomarkers to reflect disease severity and predict disease course is therefore large. We investigated whether cytokines in mucosal tissue and serum reflect clinical disease severity at the onset of UC and predict the future disease course. Methods:We prospectively monitored 102 patients from the onset of UC during 3 years, and they were followed up yearly for clinical and biochemical disease severity. Rectal biopsies were obtained from healthy controls and patients with UC. Serum and stool samples were obtained from patients with UC. Total mRNA from biopsies was analyzed with real-time PCR. Cytokine levels in serum were determined using Luminex or ELISA. Results:Mucosal mRNA expression of IL-17A was 99.8 times higher while IFN-&ggr; and IL-13 expression was increased 12.4 and 6.7 times, respectively, in patients relative to controls. Serum IL-17A correlated with clinical disease severity at the onset. Also, contrary to a number of other parameters, serum IL-17A at the onset predicted the clinical and biochemical course of the disease, as reflected by the Mayo score, number × severity of flares, and fecal calprotectin levels, respectively, during 3 years after the onset of the disease. None of these associations were found with mucosal cytokines at the onset. Conclusions:Serum IL-17A levels of treatment-naive patients with UC reflect clinical disease severity at the onset of the disease and also predicted the disease course over the following 3 years. Thus, serum IL-17A may be valuable in the clinical management of patients with UC at the onset of the disease.
Differential regulation of c‐Jun by ERK and JNK during PC12 cell differentiation

The two MAP kinases JNK and ERK direct distinct cellular activities even though they share a number of common substrates, including several transcription factors. Here we have compared JNK and ERK signalling during PC12 cell differentiation and investigated how activation of c‐Jun by the MAPKs contributes to this cellular response. Exposure to nerve growth factor, or expression of constitutively active MEK1—two treatments which cause differentiation of PC12 cells into a neuronal phenotype—result in activation of ERK‐type MAP kinases and phosphorylation of c‐Jun on several sites including Ser63 and Ser73. Constitutively activated c‐Jun, which mimics the MAPK‐phosphorylated form of the protein, can induce neuronal differentiation of PC12 cells independently of upstream signals. Conversely, expression of dominant‐negative c‐JunbZIP prevents neurite outgrowth induced by activated MEK1. Activation of MEKK1, which stimulates the JNK pathway, is not sufficient for PC12 cell differentiation but can induce apoptosis. However, neurite outgrowth is triggered when c‐Jun is co‐expressed with activated MEKK1 or SEK1. Consistently, MEK‐induced ERK activation in PC12 cells induces c‐Jun expression, while JNK signalling does not. Therefore, dual input of expression and phosphorylation of c‐Jun provided by the ERK pathway is required to direct neuronal differentiation in PC12 cells.
PHYTOTOXICITY OF PHOTOSYSTEM II (PSII) HERBICIDES TO CORAL

Recent reports of contamination of the Great Barrier Reef Marine Park by herbicides used in antifouling paints and in agriculture have caused concern over the possible effects on corals in nearshore areas. Pulse-Amplitude Modulated (PAM) chlorophyll fluorescence techniques were used to examine changes in the maximum effective quantum yield (ΔF/Fm′) of symbiotic dinoflagellates within the host tissues (in hospite) of the coral Seriatopora hystrix exposed to a number of Photosystem II (PSII) inhibiting herbicides in short-term toxicity tests. The concentration of herbicide required to reduce ΔF/Fm′ by 50% (median effective concentration [EC50]) differed by over 2 orders of magnitude: Irgarol 1051 (0.7 μg l-1) > ametryn (1.7 μg l-1) > diuron (2.3 μg l-1) > hexazinone (8.8 μg l -1) > atrazine (45 μg l-1) > simazine (150 μg l-1) > tebuthiuron (175 μg l-1) > ionynil (> 1 mg l-1). Similar absolute and relative toxicities were observed with colonies of the coral Acropora formosa (Irgarol 1051 EC50: 1.3 μg l-1, diuron EC50: 2.8 μg l-1), Time-course experiments indicated that ΔF/Fm′ was rapidly reduced (i.e. within minutes) in S. hystrix exposed to Irgarol 1051 and diuron. On return to fresh running seawater, ΔF/Fm′ recovered quickly in diuron-exposed corals (i.e. in minutes to hours), but slowly in corals exposed to Irgarol 1051 (i.e. hours to days). Time-course experiments indicated that the effects of diuron (3 μg l-1) on S. hystrix were inversely related to temperature over the range 20 to 30 °C, although initially the effects were less at the lower temperatures. Repeated exposure to pulses of Irgarol 1051 (daily 2 h exposure to 30 μg l -1 over 4 d) resulted in a 30% decrease in the density of symbiotic dinoflagellates in the tissues of S. hystrix.
On central critical values of the degree four L-functions for GSp (4): the fundamental lemma, II

We propose a new relative trace formula concerning the central critical values of the spinor $L$-functions for GSp (4). The main result is a proof of the fundamental lemma for the unit element of the Hecke algebra. Our new relative trace formula has some significant advantages over the previous ones for the subsequent development.
Perceptual and neural consequences of rapid motion adaptation

Nervous systems adapt to the prevailing sensory environment, and the consequences of this adaptation can be observed in the responses of single neurons and in perception. Given the variety of timescales underlying events in the natural world, determining the temporal characteristics of adaptation is important to understanding how perception adjusts to its sensory environment. Previous work has shown that neural adaptation can occur on a timescale of milliseconds, but perceptual adaptation has generally been studied over relatively long timescales, typically on the order of seconds. This disparity raises important questions. Can perceptual adaptation be observed at brief, functionally relevant timescales? And if so, how do its properties relate to the rapid adaptation seen in cortical neurons? We address these questions in the context of visual motion processing, a perceptual modality characterized by rapid temporal dynamics. We demonstrate objectively that 25 ms of motion adaptation is sufficient to generate a motion aftereffect, an illusory sensation of movement experienced when a moving stimulus is replaced by a stationary pattern. This rapid adaptation occurs regardless of whether the adapting motion is perceived. In neurophysiological recordings from the middle temporal area of primate visual cortex, we find that brief motion adaptation evokes direction-selective responses to subsequently presented stationary stimuli. A simple model shows that these neural responses can explain the consequences of rapid perceptual adaptation. Overall, we show that the motion aftereffect is not merely an intriguing perceptual illusion, but rather a reflection of rapid neural and perceptual processes that can occur essentially every time we experience motion.
Minus class groups of the fields of the l-th roots of unity

We show that for any prime number l > 2 the minus class group of the field of the l-th roots of unity Q p (ζl) admits a finite free resolution of length 1 as a module over the ring Z[G]/(1 + i). Here i denotes complex conjugation in G = Gal(Q p (ζl)/Q p ) ≅ (Z/lZ)*. Moreover, for the primes l < 509 we show that the minus class group is cyclic as a module over this ring. For these primes we also determine the structure of the minus class group.
Assay Establishment and Validation of a High-Throughput Screening Platform for Three-Dimensional Patient-Derived Colon Cancer Organoid Cultures

The application of patient-derived three-dimensional culture systems as disease-specific drug sensitivity models has enormous potential to connect compound screening and clinical trials. However, the implementation of complex cell-based assay systems in drug discovery requires reliable and robust screening platforms. Here we describe the establishment of an automated platform in 384-well format for three-dimensional organoid cultures derived from colon cancer patients. Single cells were embedded in an extracellular matrix by an automated workflow and subsequently self-organized into organoid structures within 4 days of culture before being exposed to compound treatment. We performed validation of assay robustness and reproducibility via plate uniformity and replicate-experiment studies. After assay optimization, the patient-derived organoid platform passed all relevant validation criteria. In addition, we introduced a streamlined plate uniformity study to evaluate patient-derived colon cancer samples from different donors. Our results demonstrate the feasibility of using patient-derived tumor samples for high-throughput assays and their integration as disease-specific models in drug discovery.
Metabolic Syndrome and Solid‐Organ Transplantation

The metabolic syndrome is proposed as a cluster of known cardiovascular risk factors, interrelated by a common pathophysiological defect, that symbolize a heightened metabolic burden. Advocates of the concept argue that it is a predictor for both diabetes and cardiovascular disease, complications of great importance posttransplantation. The abundant medical literature on the topic is now expanding into the field of transplantation with evidence linking the metabolic syndrome to adverse patient and graft outcomes. Although the implications posttransplantation are significant, controversy surrounds the concept and the topic has not previously been reviewed in the context of solid‐organ transplantation. The purpose of this review is to update transplant clinicians with our current understanding of the metabolic syndrome, review the transplantation literature and examine the controversies surrounding the concept.
Trump Tweets and the Efficient Market Hypothesis

In a Semi-Strong Form (SSF) Efficient Market, asset prices should respond quickly and completely to the public release of new information. In the period from his election on 11/8/16 and his swearing in ceremony on 1/20/17, President-elect Trump posted numerous statements (‘tweets’) on his Twitter messaging service account that identified ten publicly traded firms. In the absence of new information, the Efficient Market Hypothesis (EMH) predicts that these announcements should have little or no price impact on the common stocks of these firms. Using standard event study methods, we find that positive (negative) content tweets elicited positive (negative) abnormal returns on the event date and virtually all of this effect is from the opening stock price to the close. Within five trading days, the CARs are no longer statistically significant. President-elect Trump’s tweets were associated with increases in trading volume and Google Search activity. Taken as a whole, the price and trading volume response, combined with Google Search activity is consistent with hypothesis that it was small/noise traders who were acting on President-elect Trump’s tweets and that their impacts were transitory.
Adaptive optics observations of asteroid 216 Kleopatra

The large main-belt asteroid (216) Kleopatra has been for long suspected to be a binary object, mainly due to its large lightcurve amplitude. However, recent observations suggest that it is a single "bone-shaped" or bi-lobated body (Ostro et al. 2000; Tanga et al. 2001). We present results obtained from ground-based adaptive optics observations, and in agreement with the radar raw-observations, the images show two prominent lobes. Making use of the MISTRAL deconvolution technique, the restored images yield a well-separated binary object. Nevertheless, the spatial resolution of the 3.6m ESO telescope is limited and a dumbbell-shaped body could yield similar features. Further simulations show that adaptive optics observations with an 8-meter class telescope analyzed with the powerful MISTRAL deconvolution technique could overcome this limitation.
Efficient parallel algorithms for tree-decomposition and related problems

An efficient parallel algorithm for the tree-decomposition problem for fixed width w is presented. The algorithm runs in time O(log/sup 3/ n) and uses O(n) processors on a concurrent-read, concurrent-write parallel random access machine (CRCW PRAM). This result can be used to construct efficient parallel algorithms for three important classes of problems: MS (monadic second-order) properties, linear EMS (extended monadic second-order) extremum problems, and enumeration problems for MS properties, for graphs of tree width at most w. The sequential time complexity of the tree-composition problem for fixed w is improved, and some implications for this improvement are stated. <<ETX>>
Test-based SPL extraction: an exploratory study

Many software systems have been developed as single products before Software Product Lines (SPLs) have emerged. Although some promising approaches have been proposed, extracting an SPL from existing software products is still expensive and time consuming. This paper presents an exploratory study that relies on a test-based SPL extraction from systems already developed. We aim to evaluate testing as the main mean to locate feature code and different sorts of existing artifacts to support the test-based location. We conduct two case studies starting from the derivation of the SPL feature model to the feature code location. Our preliminary results indicate (i) good rates of precision for feature seed location, where seed means a small portion of the feature code that allows the identification of the remaining portion, and (ii) good rates of recall for locating the whole feature code.
Common heritable contributions to low-risk trauma, high-risk trauma, posttraumatic stress disorder, and major depression.

CONTEXT Understanding the relative contributions of genetic and environmental factors to trauma exposure, posttraumatic stress disorder (PTSD), and major depressive disorder (MDD) is critical to developing etiologic models of these conditions and their co-occurrence. OBJECTIVES To quantify heritable influences on low-risk trauma, high-risk trauma, PTSD, and MDD and to estimate the degree of overlap between genetic and environmental sources of variance in these 4 phenotypes. DESIGN Adult twins and their siblings were ascertained from a large population-based sample of female and male twin pairs on the basis of screening items for childhood sexual abuse and physical abuse obtained in a previous assessment of this cohort. SETTING Structured psychiatric telephone interviews. PARTICIPANTS Total sample size of 2591: 996 female and 536 male twins; 625 female and 434 male nontwin siblings. MAIN OUTCOME MEASURE Lifetime low- and high-risk trauma exposure, PTSD, and MDD. RESULTS In the best-fitting genetic model, 47% of the variance in low-risk trauma exposure and 60% of the variance in high-risk trauma exposure was attributable to additive genetic factors. Heritable influences accounted for 46% of the variance in PTSD and 27% of the variance in MDD. An extremely high degree of genetic overlap was observed between high-risk trauma exposure and both PTSD (r = 0.89; 95% CI, 0.78-0.99) and MDD (r = 0.89; 95% CI, 0.77-0.98). Complete correlation of genetic factors contributing to PTSD and to MDD (r = 1.00) was observed. CONCLUSIONS The evidence suggests that almost all the heritable influences on high-risk trauma exposure, PTSD, and MDD, can be traced to the same sources; that is, genetic risk is not disorder specific. Individuals with a positive family history of either PTSD or MDD are at elevated risk for both disorders and should be closely monitored after a traumatic experience for symptoms of PTSD and MDD.
Nurses' knowledge regarding hand hygiene and its individual and organizational predictors.

INTRODUCTION Based on recommendations from World Health Organization, hand hygiene is the most important way to control the hospital infections. Due to the critical role of nurses in patient care, they should have essential and updated information regarding hand hygiene. So this study aims at determining the knowledge of hand hygiene and its individual and organizational predictors among nurses in neonatal units. METHODS This descriptive and cross-sectional study was conducted in neonatal units in the hospitals affiliated to Tabriz University of Medical Sciences. The participants surveyed in this study were 150 nurses who were invited by census sampling method. A researcher prepared questionnaire that investigated the knowledge of participants about hand hygiene and was used after approving its validity and reliability. The quantitative analysis of this study used Statistical Package for Social Sciences SPSS version 13 by descriptive statistics and pearson correlation test, independent samples t-test, One-way ANOVA. For multivariable explanation of nurses' knowledge based on independent variables multiple linear regressions was used. RESULTS Most of participants have an acceptable level of knowledge regarding hand hygiene. The highest score was for infection control domain and the lowest score was for definition of hand hygiene domain. Multivariable analysis showed that work experience and history of previous training were the most important predictors of participants' knowledge about hand hygiene. CONCLUSION It is recommended that infection control committees should revise their educational methods and give more emphasis on update guidelines regarding hand hygiene. Also, more experienced nurses should be employed in neonatal units.
Field Experiments in Strategy Research

Strategy research often aims to empirically establish a causal relationship between an independent variable and a dependent variable such as firm performance. For many important strategy research questions, however, traditional empirical techniques are not sufficient to establish causal effects with high confidence. We propose that field experiments have potential to be used more widely in strategy research, leveraging methodological innovations from other disciplines to address persistent puzzles in the literature. We first review the advantages and disadvantages of using field experiments to answer questions in strategy. We define two types of experiments, "strategy field experiments" and "process field experiments," and present an original example of each variety. The first study explores the liability of foreignness and the second study tests theories regarding corporate culture.