Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncovering Suitable Reference Proteins for Expression Studies in Human Adipose Tissue with Relevance to Obesity

Background Protein expression studies based on the two major intra-abdominal human fat depots, the subcutaneous and the omental fat, can shed light into the mechanisms involved in obesity and its co-morbidities. Here we address, for the first time, the identification and validation of reference proteins for data standardization, which are essential for accurate comparison of protein levels in expression studies based on fat from obese and non-obese individuals. Methodology and Findings To uncover adipose tissue proteins equally expressed either in omental and subcutaneous fat depots (study 1) or in omental fat from non-obese and obese individuals (study 2), we have reanalyzed our previously published data based on two-dimensional fluorescence difference gel electrophoresis. Twenty-four proteins (12 in study 1 and 12 in study 2) with similar expression levels in all conditions tested were selected and identified by mass spectrometry. Immunoblotting analysis was used to confirm in adipose tissue the expression pattern of the potential reference proteins and three proteins were validated: PARK7, ENOA and FAA. Western Blot analysis was also used to test customary loading control proteins. ENOA, PARK7 and the customary loading control protein Beta-actin showed steady expression profiles in fat from non-obese and obese individuals, whilst FAA maintained steady expression levels across paired omental and subcutaneous fat samples. Conclusions ENOA, PARK7 and Beta-actin are proper reference standards in obesity studies based on omental fat, whilst FAA is the best loading control for the comparative analysis of omental and subcutaneous adipose tissues either in obese and non-obese subjects. Neither customary loading control proteins GAPDH and TBB5 nor CALX are adequate standards in differential expression studies on adipose tissue. The use of the proposed reference proteins will facilitate the adequate analysis of proteins differentially expressed in the context of obesity, an aim difficult to achieve before this study.
Body Temperature, Blood Infection Parameters, and Outcome of Thrombolysis-Treated Ischemic Stroke Patients

Background and Aims Body temperature, inflammation, and infections may modify response to thrombolytic therapy. We studied their associations with clinical improvement after intravenous thrombolysis and three-month outcome. Methods We included 985 consecutive acute ischemic stroke patients treated with intravenous thrombolysis at the Helsinki University Central Hospital during 1995–2008. Body temperature, blood leukocyte count, and C-reactive protein levels were analyzed on arrival and at day one. Clinical improvement was defined as National Institutes of Health Stroke Scale score decrease of ≥4 points or a score of 0 at 24 h. Functional outcome was assessed at three-months with the modified Rankin Scale dichotomized at 0–2 (good) vs. 3–6 (poor). Associations were tested with multivariable logistic regression analysis. Results Of the baseline variables, lower C-reactive protein independently predicted clinical improvement at 24 h (odds ratio 0·94 per 5 mg/L; 95% confidence interval 0·89–1·00; P = 0·03), whereas higher leukocyte count (odds ratio 1·10 per E9/L; 1·03–1·17; P < 0·01) and C-reactive protein (odds ratio 1·07 per 5 mg/L; 1·01–1·14; P = 0·02) were associated with poor three-month outcome. When body temperature increased over the first 24 h, clinical improvement after thrombolysis was unlikely (odds ratio 0·66 per °C; 0·45–0·95; P = 0·03) and poor outcome more common (odds ratio 1·63 per °C; 1·24–2·14; P < 0·001). Elevated leukocytes at baseline increased the risk of symptomatic intracerebral hemorrhage (odds ratio 1·07 per E9/L; 1·00–1·13; P= 0·04). Conclusion A lower level of systemic inflammation at time of thrombolysis may be associated with clinical improvement and good outcome at three-months. Increase in body temperature during the first 24 h associates with lack of clinical improvement and worse patient outcome.
Control of a brain–computer interface using stereotactic depth electrodes in and adjacent to the hippocampus

A brain–computer interface (BCI) is a device that enables severely disabled people to communicate and interact with their environments using their brain waves. Most research investigating BCI in humans has used scalp-recorded electroencephalography or intracranial electrocorticography. The use of brain signals obtained directly from stereotactic depth electrodes to control a BCI has not previously been explored. In this study, event-related potentials (ERPs) recorded from bilateral stereotactic depth electrodes implanted in and adjacent to the hippocampus were used to control a P300 Speller paradigm. The ERPs were preprocessed and used to train a linear classifier to subsequently predict the intended target letters. The classifier was able to predict the intended target character at or near 100% accuracy using fewer than 15 stimulation sequences in the two subjects tested. Our results demonstrate that ERPs from hippocampal and hippocampal adjacent depth electrodes can be used to reliably control the P300 Speller BCI paradigm.
The risk factor profile of patients undergoing cardiovascular surgery and their relatives *

*Laboratory for Atherosclerosis Research, Institute for Clinical and Experimental Medicine, Prague, **Department of Cardiac Surgery, âeské Budûjovice Hospital, âeské Budûjovice, ***Department of Statistics, Institute for Clinical and Experimental Medicine, ****Cardiocenter, Department of Cardiology, Královské Vinohrady University Hospital and Charles University Medical School 3, Prague, Czech Republic
Relative Salience of Speech Rhythm and Speech Rate on Perceived Foreign Accent in a Second Language

We investigated the independent contribution of speech rate and speech rhythm to perceived foreign accent. To address this issue we used a resynthesis technique that allows neutralizing segmental and tonal idiosyncrasies between identical sentences produced by French learners of English at different proficiency levels and maintaining the idiosyncrasies pertaining to prosodic timing patterns. We created stimuli that (1) preserved the idiosyncrasies in speech rhythm while controlling for the differences in speech rate between the utterances; (2) preserved the idiosyncrasies in speech rate while controlling for the differences in speech rhythm between the utterances; and (3) preserved the idiosyncrasies both in speech rate and speech rhythm. All the stimuli were created in intoned (with imposed intonational contour) and flat (with monotonized, constant F0) conditions. The original and the resynthesized sentences were rated by native speakers of English for degree of foreign accent. We found that both speech rate and speech rhythm influence the degree of perceived foreign accent, but the effect of speech rhythm is larger than that of speech rate. We also found that intonation enhances the perception of fine differences in rhythmic patterns but reduces the perceptual salience of fine differences in speech rate.
Quantification of mutant alleles in circulating tumor DNA can predict survival in lung cancer

Purpose We aimed to investigate the feasibility of droplet digital PCR (ddPCR) for the quantitative and dynamic detection of EGFR mutations and next generation sequencing (NGS) for screening EGFR-tyrosine kinase inhibitors (EGFR-TKIs) resistance-relevant mutations in circulating tumor DNA (ctDNA) from advanced lung adenocarcinoma (ADC) patients. Results Detection limit of EGFR mutation in ctDNA by ddPCR was 0.04%. Taking the EGFR mutation in tumor tissue as the golden standard, the concordance of EGFR mutations detected in ctDNA was 74% (54/73). Patients with EGFR mutation in ctDNA (n = 54) superior progression-free survival (PFS, median, 12.6 vs. 6.7 months, P < 0.001) and overall survival (OS, median, 35.6 vs. 23.8 months, P = 0.028) compared to those with EGFR wild type in ctDNA (n = 19). Patients with high EGFR-mutated abundance in ctDNA (> 5.15%) showed better PFS compared to those with low EGFR mutated abundance (≤ 5.15%) (PFS, median, 15.4 vs. 11.1 months, P = 0.021). NGS results showed that 66.6% (8/12) total mutational copy number were elevated and 76.5% (26/34) mutual mutation frequency increased after disease progression. Methods Seventy-three advanced ADC patients with tumor tissues carrying EGFR mutations and their matched pre- and post-EGFR-TKIs plasma samples were enrolled in this study. Absolute quantities of plasma EGFR mutant and wild-type alleles were measured by ddPCR. Multi-genes testing was performed using NGS in 12 patients. Conclusions Dynamic and quantitative analysis of EGFR mutation in ctDNA could guide personalized therapy for advanced ADC. NGS shows good performance in multiple genes testing especially novel and uncommon genes.
Semi-Supervised Methods to Predict Patient Survival from Gene Expression Data

An important goal of DNA microarray research is to develop tools to diagnose cancer more accurately based on the genetic profile of a tumor. There are several existing techniques in the literature for performing this type of diagnosis. Unfortunately, most of these techniques assume that different subtypes of cancer are already known to exist. Their utility is limited when such subtypes have not been previously identified. Although methods for identifying such subtypes exist, these methods do not work well for all datasets. It would be desirable to develop a procedure to find such subtypes that is applicable in a wide variety of circumstances. Even if no information is known about possible subtypes of a certain form of cancer, clinical information about the patients, such as their survival time, is often available. In this study, we develop some procedures that utilize both the gene expression data and the clinical data to identify subtypes of cancer and use this knowledge to diagnose future patients. These procedures were successfully applied to several publicly available datasets. We present diagnostic procedures that accurately predict the survival of future patients based on the gene expression profile and survival times of previous patients. This has the potential to be a powerful tool for diagnosing and treating cancer.
HLA class I and class II polymorphisms in Tunisian Berbers

Background: The HLA polymorphism is a powerful genetic tool to study population origins. By analysing allele frequencies and haplotypes in different populations, it is possible to identify ethnic groups and establish the genetic relationships among them. Aim: The Berber (endogenous Tunisians) HLA class I and class II genotypes were analysed and compared with those of Mediterranean and Sub-Saharan African communities using genetic distances, Neighbour-Joining dendrograms, correspondence and haplotype analysis. Subjects and methods: One hundred and five unrelated Berbers were typed for HLA class I (A, B) and class II (DRB1, DQB1) gene alleles using reverse dot-blot hybridization. Results: High frequencies of A*0201 (24.76%), A*3402 (22.38%) and B*44 (32.85%) alleles were recorded for Berbers, the highest recorded for Mediterranean and North African populations. This study shows a close relatedness of Tunisian Berbers to other Tunisians, North Africans and Iberians. Conclusion: The apparent relatedness of Tunisian Berbers to present-day (North African) Tunisians, Algerians and Moroccans suggests that the Arab invasion of North Africa (7th–11th centuries AD) did not significantly impact the genetic makeup of North Africans. Furthermore, Tunisian Berbers appear to be closely related to Iberians (Spaniards and Basques), indicating that the 7th century AD gene flow of invaders was low in Iberians and that the main part of their genetic pool came after the Northward Saharan migration, when hyper-arid conditions were established in Sahara (before 6000 BC). Other studied populations belong to the old Mediterranean substratum, which has been present in the area since pre-Neolithic times. This study indicates a higher proportion of Iberian than Arab ancestry in Tunisian Berbers, which is of value in evaluating the evolutionary history of present-day Tunisians. Greeks seem to share genetic HLA features (Chr 6) with Sub-Saharans. The relatedness of Greeks to Sub-Saharans has been confirmed by other studies based on chromosome 7 genetic markers.
An Effectiveness Study of a Culturally Enriched School-Based CBT Anxiety Prevention Program

Anxiety disorders are prevalent in the school-aged population and are present across cultural groups. Scant research exists on culturally relevant prevention and intervention programs for mental health problems in the Aboriginal populations. An established cognitive behavioral program, FRIENDS for Life, was enriched to include content that was culturally relevant to Aboriginal students. Students (N = 533), including 192 students of Aboriginal background, participated in the cluster randomized control study. Data were collected three times over 1 year. A series of multilevel models were conducted to examine the effect of the culturally enriched FRIENDS program on anxiety. These analyses revealed that the FRIENDS program did not effectively reduce anxiety for the total sample or for Aboriginal children specifically. However, all students, regardless of intervention condition, Aboriginal status, or gender, reported a consistent decrease in feelings of anxiety over the 6-month study period.
An epidemic approach to dependable key-value substrates

The sheer volumes of data handled by today's Internet services demand uncompromising scalability from the persistence substrates. Such demands have been successfully addressed by highly decentralized key-value stores invariably governed by a distributed hash table. The availability of these structured overlays rests on the assumption of a moderately stable environment. However, as scale grows with unprecedented numbers of nodes the occurrence of faults and churn becomes the norm rather than the exception, precluding the adoption of rigid control over the network's organization. In this position paper we outline the major ideas of a novel architecture designed to handle today's very large scale demand and its inherent dynamism. The approach rests on the well-known reliability and scalability properties of epidemic protocols to minimize the impact of churn. We identify several challenges that such an approach implies and speculate on possible solutions to ensure data availability and adequate access performance.
AlignedReID: Surpassing Human-Level Performance in Person Re-Identification

In this paper, we propose a novel method called AlignedReID that extracts a global feature which is jointly learned with local features. Global feature learning benefits greatly from local feature learning, which performs an alignment/matching by calculating the shortest path between two sets of local features, without requiring extra supervision. After the joint learning, we only keep the global feature to compute the similarities between images. Our method achieves rank-1 accuracy of 94.4% on Market1501 and 97.8% on CUHK03, outperforming state-of-the-art methods by a large margin. We also evaluate human-level performance and demonstrate that our method is the first to surpass human-level performance on Market1501 and CUHK03, two widely used Person ReID datasets.
The regulation of competence to replicate in meiosis by Cdc6 is conserved during evolution

DNA replication licensing is an important step in the cell cycle at which cells become competent for DNA replication. When the cell cycle is arrested for long periods of time, this competence is lost. This is the case for somatic cells arrested in G0 or vertebrate oocytes arrested in G2. CDC6 is a factor involved in replication initiation competence which is necessary for the recruitment of the MCM helicase complex to DNA replication origins. In Xenopus, we have previously shown that CDC6 is the only missing replication factor in the oocyte whose translation during meiotic maturation is necessary and sufficient to confer DNA replication competence to the egg before fertilization (Lemaitre et al., 2002: Mol Biol Cell 13:435–444; Whitmire et al., 2002: Nature 419:722–725). Here, we report that this oogenesis control has been acquired by metazoans during evolution and conserved up to mammals. We also show that, contrary to eukaryotic metazoans, in S. pombe cdc18 (the S. pombe CDC6 homologue), CDC6 protein synthesis is down regulated during meiosis. As such, the lack of cdc18 prevents DNA replication from occurring in spores, whereas the presence of cdc6 makes eggs competent for DNA replication. Mol. Reprod. Dev. 69: 94–100, 2004. © 2004 Wiley‐Liss, Inc.
Privacy in the Sharing Economy

Contemporary C2C platforms, such as Airbnb, have exhibited considerable growth in recent years and are projected to continue doing so in the future. These novel consumer-to-consumer marketplaces have started to obliterate the boundaries between private and economic spheres. Marketing personal resources online is inherently associated with the disclosure of personal and sometimes intimate information. This raises unprecedented questions of privacy. Yet, there is so far little research on the role of privacy considerations in the sharing economy literature. Leveraging the theoretical perspective of privacy calculus, we address this gap by investigating how privacy concerns and economic prospects shape a potential provider’s intentions to share via different communication channels. We relate privacy concerns back to the provider’s perceptions of the audience. We evaluate our research model by means of a scenario-based online survey, providing broad support for our reasoning.
Multi-level organization and summarization of the discovered rules

Many existing data mining techniques often p roduce a large number of rules, which make it very difficult for manual inspection o f the rules to identify those interesting ones. This problem represents a major gap between the results of data mining and the understanding and use of the mining results. In this paper, we a rgue that t he key problem is not with the large number of rules because if there are indeed many rules that exist in data, they should b e discovered. The main p roblem is with ou r inability to organize, summarize and present the rules in such a way that they can b e ea sily analyzed b y the user. In this paper, we propose a technique to intuitively organize a nd summarize the discovered rules. With this organization, the discovered rules can b e presented to the user in the way as we think and talk about knowledge in ou r daily lives. This organization also allows the user to view the discovered rules at different levels of details, and to focus his/her attention on those interesting aspects. This paper presents this technique a nd u ses it t o o rganize, summarize a nd present t he knowledge e mbedded in a decision tree, and a set of association rules. Experiment results and p ractical applications show that the technique is both intuitive and effective.
Genetic modifications of voltage-sensitive sodium channels in Drosophila: gene dosage studies of the seizure locus

We have identified a genetic locus in Drosophila melanogaster whose product appears to have a structural role in the formation of functional voltage-sensitive sodium channels. This locus, designated seizure, is defined by two temperature-sensitive alleles (seits-1 and seits-2), each of which causes convulsive seizures followed by a rapid but reversible paralysis of adults at restrictive temperatures above 38 degrees C. Previous work had shown that seits-2 extracts display an altered pH dependence and an abnormally high Kd for [3H]-saxitoxin binding at high temperatures, suggesting that sodium channels in seits- 2 mutants have an altered structure (Jackson F. R., S. D. Wilson, G. R. Strichartz, and L. M. Hall (1984) Nature 308: 189–191). These binding studies have now been extended to extracts of seits-1 which have a Kd not significantly different from wild-type at all assay temperatures. However, seits-1 extracts show a reduced number of saxitoxin binding sites (Bmax) relative to wild-type. This reduction is only 5 to 18% at 0 degree C but is 17 to 37% at 39 degrees C, suggesting that under certain conditions sodium channels in the seits-1 mutant are more labile than those of wild-type. Cytogenetic studies demonstrate that the seizure locus maps within region 60A to 60B8–10 on the second chromosome. Gene dosage analysis of approximately 99.7% of the genome, including this second chromosome region, failed to detect a wild-type locus whose dose affected saxitoxin-binding activity. Nevertheless, the mutant seits-2 allele has codominant and dose-dependent effects on paralytic behavior and saxitoxin-binding activity.
Rad4 Mainly Functions in Chk1-Mediated DNA Damage Checkpoint Pathway as a Scaffold Protein in the Fission Yeast Schizosaccharomyces pombe

Rad4/Cut5 is a scaffold protein in the Chk1-mediated DNA damage checkpoint in S. pombe. However, whether it contains a robust ATR-activation domain (AAD) required for checkpoint signaling like its orthologs TopBP1 in humans and Dpb11 in budding yeast has been incompletely clear. To identify the putative AAD in Rad4, we carried out an extensive genetic screen looking for novel mutants with an enhanced sensitivity to replication stress or DNA damage in which the function of the AAD can be eliminated by the mutations. Two new mutations near the N-terminus were identified that caused significantly higher sensitivities to DNA damage or chronic replication stress than all previously reported mutants, suggesting that most of the checkpoint function of the protein is eliminated. However, these mutations did not affect the activation of Rad3 (ATR in humans) yet eliminated the scaffolding function of the protein required for the activation of Chk1. Several mutations were also identified in or near the recently reported AAD in the C-terminus of Rad4. However, all mutations in the C-terminus only slightly sensitized the cells to DNA damage. Interestingly, a mutant lacking the whole C-terminus was found resistant to DNA damage and replication stress almost like the wild type cells. Consistent with the resistance, all known Rad3 dependent phosphorylations of checkpoint proteins remained intact in the C-terminal deletion mutant, indicating that unlike that in Dpb11, the C-terminus of Rad4 does not contain a robust AAD. These results, together with those from the biochemical studies, show that Rad4 mainly functions as a scaffold protein in the Chk1, not the Cds1(CHK2 in humans), checkpoint pathway. It plays a minor role or is functionally redundant with an unknown factor in Rad3 activation.
A class of flow bifurcation models with lognormal distribution and fractal dispersion.

We report a quantitative analysis of a simple dichotomous branching tree model for blood flow in vascular networks. Using the method of moment-generating function and geometric Brownian motion from stochastic mathematics, our analysis shows that a vascular network with asymmetric branching and random variation at each bifurcating point gives rise to an asymptotic lognormal flow distribution with a positive skewness. The model exhibits a fractal scaling in the dispersion of the regional flow in the branches. Experimentally measurable fractal dimension of the relative dispersion in regional flow is analytically calculated in terms of the asymmetry and the variance at local bifurcation; hence the model suggests a powerful method to obtain the physiological information on local flow bifurcation in terms of flow dispersion analysis. Both the fractal behavior and the lognormal distribution are intimately related to the fact that it is the logarithm of flow, rather than flow itself, which is the natural variable in the tree models. The kinetics of tracer washout is also discussed in terms of the lognormal distribution.