Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of a 44 Gene Classifier for the Evaluation of Chronic Fatigue Syndrome from Peripheral Blood Mononuclear Cell Gene Expression

Chronic fatigue syndrome (CFS) is a clinically defined illness estimated to affect millions of people worldwide causing significant morbidity and an annual cost of billions of dollars. Currently there are no laboratory-based diagnostic methods for CFS. However, differences in gene expression profiles between CFS patients and healthy persons have been reported in the literature. Using mRNA relative quantities for 44 previously identified reporter genes taken from a large dataset comprising both CFS patients and healthy volunteers, we derived a gene profile scoring metric to accurately classify CFS and healthy samples. This metric out-performed any of the reporter genes used individually as a classifier of CFS. To determine whether the reporter genes were robust across populations, we applied this metric to classify a separate blind dataset of mRNA relative quantities from a new population of CFS patients and healthy persons with limited success. Although the metric was able to successfully classify roughly two-thirds of both CFS and healthy samples correctly, the level of misclassification was high. We conclude many of the previously identified reporter genes are study-specific and thus cannot be used as a broad CFS diagnostic.
Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea

A critical assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We also demonstrate a strong selection for avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.
Optic-flow selective cortical sensory regions associated with self-reported states of vection

Optic flow is one of the most important visual cues to the estimation of self-motion. It has repeatedly been demonstrated that a cortical network including visual, multisensory, and vestibular areas is implicated in processing optic flow; namely, visual areas middle temporal cortex (MT+), V6; multisensory areas ventral intra-parietal area (VIP), cingulate sulcus visual area, precuneus motion area (PcM); and vestibular areas parieto-insular vestibular cortex (PIVC) and putative area 2v (p2v). However, few studies have investigated the roles of and interaction between the optic-flow selective sensory areas within the context of self-motion perception. When visual information (i.e., optic flow) is the sole cue to computing self-motion parameters, the discrepancy amongst the sensory signals may induce an illusion of self-motion referred to as ‘vection. ’ This study aimed to identify optic-flow selective sensory areas that are involved in the processing of visual cues to self-motion, by introducing vection as an index and assessing activation in which of those areas reflect vection, using functional magnetic resonance imaging. The results showed that activity in visual areas MT+ and V6, multisensory area VIP and vestibular area PIVC was significantly greater while participants were experiencing vection, as compared to when they were experiencing no vection, which may indicate that activation in MT+, V6, VIP, and PIVC reflects vection. The results also place VIP in a good position to integrate visual cues related to self-motion and vestibular information.
Statistical source expansion for question answering

A source expansion algorithm automatically extends a given text corpus with related content from large external sources such as the Web. The expanded corpus is not intended for human consumption but can be used in question answering (QA) and other information retrieval or extraction tasks to find more relevant information and supporting evidence. We propose an algorithm that extends a corpus of seed documents with web content, using a statistical model to select text passages that are both relevant to the topics of the seeds and complement existing information. In an evaluation on 1,500 hand-labeled web pages, our algorithm ranked text passages by relevance with 81% MAP, compared to 43% when relying on web search engine ranks alone and 75% when using a multi-document summarization algorithm. Applied to QA, the proposed method yields consistent and significant performance gains. We evaluated the impact of source expansion on over 6,000 questions from the Jeopardy! quiz show and TREC evaluations using Watson, a state-of-the-art QA system. Accuracy increased from 66% to 71% on Jeopardy! questions and from 59% to 64% on TREC questions.
Asymptotic experimental analysis for the Held-Karp traveling salesman bound

The Held-Karp (HK) lower bound is the solution to the linear programming relaxation of the standard integer programming formulation of the traveling salesman problem (TSP). For numbers of cities N up to 30,000 or more it can be computed exactly using the Simplex method and appropriate separation algorithms, and for N up to a million good approximations can be obtained via iterative Lagrangean relaxation techniques first suggested by Held and Karp. In this paper, we consider three applications of our ability to compute/approximate this bound. First, we provide empirical evidence in support of using the HK bound as a stand-in for the optimal tour length when evaluating the quality of near-optimal tours. We show that for a wide variety of randomly generated instance types the optimal tour length averages less than 0.8% over the HK bound, and even for the real-world instances in TSPLIB the gap is almost always less than 2%. Moreover, our data indicates that the HK bound can provide substantial ‘‘variance reduction’’ in experimental studies involving randomly generated instances. Second, we estimate the expected HK bound as a function of N for a variety of random instance types, based on extensive computations. For example, for random Euclidean instances it is known that the ratio of the HeldKarp bound to √+ + N approaches a constant C HK, and we estimate both that constant and the rate of convergence to it. Finally, we combine this information with our earlier results on expected HK gaps to obtain estimates for expected optimal tour lengths. For random Euclidean instances, we conclude that C OPT, the limiting ratio of the optimal tour length to √+ + N , is . 7124 ± . 0002, thus invalidating the commonly cited estimates of . 749 and . 765 and undermining many claims of good heuristic performance based on those estimates. For random distance matrices, the expected optimal tour length appears to be about 2.042, adding support to a conjec
On the Capacity of Secure Network Coding

We consider the problem of using a multicast network code to transmit information securely in the presence of a “wire-tap” adversary who can eavesdrop on a bounded number of network edges. Cai & Yeung (ISIT, 2002) gave a method to alter any given linear network code into a new code that is secure. However, their construction is in general inefficient, and requires a very large field size; in many cases this is much greater than the field size required by standard network code construction algorithms to achieve the min-cut capacity (without a security guarantee). In this paper we generalize and simplify the method of Cai & Yeung, and show that the problem of making a linear network code secure is equivalent to the problem of finding a linear code with certain generalized distance properties. We show that if we give up a small amount of overall capacity, then a random code achieves these properties using a much smaller field size — in some cases a field of constant size suffices — than the construction of Cai & Yeung. We add further support to this approach by showing that if we are not willing to give up any capacity, then a large field size may sometimes be required to achieve security.
Identification of multiple subclones in peripheral T-cell lymphoma, not otherwise specified with genomic aberrations

Peripheral T‐cell lymphoma, not otherwise specified (PTCL, NOS) with genomic aberrations has been shown to resemble lymphoma‐type adult T‐cell leukemia/lymphoma (ATLL) in terms of its genomic aberration patterns, histopathology, and prognosis. We have shown recently that a majority of patients with acute‐type ATLL have multiple subclones that were likely produced in lymph nodes. In this study, we analyzed whether PTCL, NOS with genomic aberrations also has multiple subclones as found in ATLL by means of high‐resolution oligo‐array comparative genomic hybridization (CGH). Thirteen cases of PTCL, NOS were available for 44K high‐resolution array CGH analysis. The results showed that 11 (84.6%) of the 13 cases had a log2 ratio imbalance, suggesting that multiple subclones exist in PTCL, NOS with genomic aberrations. In order to analyze the association between multiple subclones and prognosis, we used previous bacterial‐artificial chromosome (BAC) array analyses for 29 cases and found that the existence of multiple subclones was associated with a poor prognosis (P = 0.0279).
Interdisciplinary collaboration between medical and non-medical professions in health and social care.

OBJECTIVES This paper addresses the issue of interdisciplinary collaboration between medical and non-medical professions in health and social care. The introduction defines basic terms such as interdisciplinary cooperation, interdisciplinary team, and health and social care. Additionally, it highlights the significance and contribution of interdisciplinary collaboration in the care of the patient/client in health and social care. The aim of the paper is to identify factors influencing the process of interdisciplinary collaboration between, in particular, social workers and physicians. In compliance with the main goal of the research, the following partial goals were included: 1) to identify factors that limit the process of interdisciplinary collaboration between social workers and physicians, and 2) to identify factors which support the process of interdisciplinary collaboration between social workers and physicians. METHODS Based on the research goals, a systematic review was selected as the research method for the paper. The research dataset consisted of articles obtained from the following databases: EBSO, PUBMED/MEDLINE, SCIENCE DIRECT and SCOPUS. The databases were search using the following keywords: interprofessional cooperation, interdisciplinary, collaboration, social work, and physicians/doctors. RESULTS Using the results, the following factors supporting interdisciplinary collaboration were identified: acknowledgement of colleagues' expertise, recognition of roles, positive level of communication, and mutual respect. Factors that limit interdisciplinary processes included the following: varying professional perspectives, theoretical differences, lack of knowledge, and poor communication.
Lung cancer.

Lung cancer was the leading cause of cancer deaths in North Carolina in 2012 (29.6%). It has been the leading cause of cancer deaths in North Carolina for over two decades. It was estimated that 8,624 people in North Carolina would be diagnosed with lung cancer and 6,180 people in North Carolina would die from lung cancer in 2014.1 The American Cancer Society reports that lung cancer death rates began declining in 1991 for men and in 2003 for women, and reflects the change in smoking patterns over the past 50 years.2
The effect of age on cerebrovascular reactivity to cold pressor test and head‐up tilt

Objectives– To compare the cold pressor test (CPT) and head‐up tilt (HUT) responses of the older and younger healthy individuals by transcranial Doppler. Subjects and methods– Forty healthy volunteers were divided into two age groups (18–39 years, 40–69 years). Mean blood velocity (vm) in both middle cerebral arteries was monitored during CPT and HUT. Mean arterial blood pressure, heart rate and end‐tidal CO2 (Et‐CO2) were measured simultaneously. Results– The vm increased by 7.1% during CPT and decreased by 10.1% during HUT. The vm responses were significantly lower in the older group (P < 0.01). Linear regression analysis showed a significant effect of age on dvm during both CPT (P < 0.01) as well as HUT (P < 0.01). Conclusion– The age affected the vm responses to CPT and HUT in the group of older subjects.
Factors Affecting Smile Esthetics

ABSTRACT Smiling has been one of the areas that draw the interest of orthodontists due to esthetic concerns in recent years. It should be understood what an ideal smile is and which factors affect it, and these should certainly be reflected in the orthodontic treatment plan. The purpose of this review is to describe smiling and to examine factors affecting smile and smile evaluation methods.
Clinical utility of visceral adipose tissue for the identification of cardiometabolic risk in white and African American adults.

BACKGROUND Visceral adipose tissue (VAT) has been identified as a harmful fat depot, and sex and race differences in VAT have been reported in white and African Americans. OBJECTIVES We determined the clinical utility of VAT in the identification of individuals at elevated cardiometabolic risk in white and African American adults and compared the clinical utility with measures obtained by using dual-energy X-ray absorptiometry (DXA) and anthropometric measures. DESIGN The sample included 429 white women, 311 African American women, 406 white men, and 100 African American men who were 18-74 y of age. VAT was measured by using computed tomography, fat mass (FM) and percentage of body fat were measured by using DXA, and waist circumference (WC) and BMI were assessed. Receiver operating characteristic curves were used to compare the utility of measures in the identification of participants in the upper quintile of a continuous score derived from principal components analysis of fasting glucose, HDL cholesterol, triglycerides, and blood pressure. RESULTS The clinical utility of measures varied across sex-by-race groups. In the overall sample, the areas under the curve were significantly higher for VAT and WC in comparison with the other indicators. Identified VAT thresholds were higher in white men (140 cm(2)) and women (141 cm(2)) than in African American men (82 cm(2)) and women (97 cm(2)). CONCLUSIONS VAT and WC showed greater clinical utility than did other obesity measures. Because of the complexity of measuring VAT, the use of WC is recommended for the identification of adults with elevated cardiometabolic risk factors. The Pennington Center Longitudinal Study was registered at clinicaltrials.gov as NCT00959270.
Arabic Handwriting Recognition Competition

This paper describes the Arabic handwriting recognition competition held at ICDAR 2007. This second competition (the first was at ICDAR 2005) again uses the IFN/ENIT-database with Arabic handwritten Tunisian town names. Today, more than 54 research groups from universities, research centers, and industry are working with this database worldwide. This year, 8 groups with 14 systems are participating in the competition. The systems were tested on known data and on two datasets which are unknown to the participants. The systems are compared on the most important characteristic, the recognition rate. Additionally, the relative speed of the different systems were compared. A short description of the participating groups, their systems, and the results achieved are finally presented.
Treating advanced hepatocellular carcinoma: How to get out of first gear

Hepatocellular carcinoma is a common malignancy with a poor prognosis. Sorafenib is the only systemic therapy known to improve the overall survival of patients with advanced disease. The clinical benefit of sorafenib is modest and the mechanistic basis for its activity is unknown. Four phase 3 clinical trials have failed to improve on sorafenib in the frontline setting and no agent has been shown to impact outcomes after sorafenib failure. Several factors have contributed to this recent stall in drug development but new approaches hold promise and currently are being investigated. This review will focus on the current pipeline of experimental therapeutics for patients with advanced hepatocellular carcinoma and shed a light on scientific limitations that hamper the advancement of new therapies for this disease, and ways around it. Cancer 2014;120:3122–3130. © 2014 American Cancer Society.
Trpv1 Reporter Mice Reveal Highly Restricted Brain Distribution and Functional Expression in Arteriolar Smooth Muscle Cells

The heat and capsaicin receptor, TRPV1, is required for the detection of painful heat by primary afferent pain fibers (nociceptors), but the extent to which functional TRPV1 channels are expressed in the CNS is debated. Because previous evidence is based primarily on indirect physiological responses to capsaicin, here we genetically modified the Trpv1 locus to reveal, with excellent sensitivity and specificity, the distribution of TRPV1 in all neuronal and non-neuronal tissues. In contrast to reports of widespread and robust expression in the CNS, we find that neuronal TRPV1 is primarily restricted to nociceptors in primary sensory ganglia, with minimal expression in a few discrete brain regions, most notably in a contiguous band of cells within and adjacent to the caudal hypothalamus. We confirm hypothalamic expression in the mouse using several complementary approaches, including in situ hybridization, calcium imaging, and electrophysiological recordings. Additional in situ hybridization experiments in rat, monkey, and human brain demonstrate that the restricted expression of TRPV1 in the CNS is conserved across species. Outside of the CNS, we find TRPV1 expression in a subset of arteriolar smooth muscle cells within thermoregulatory tissues. Here, capsaicin increases calcium uptake and induces vasoconstriction, an effect that likely counteracts the vasodilation produced by activation of neuronal TRPV1.
Thioredoxin in Allergic Inflammation

Thioredoxin (TRX) is a redox-active protein that regulates reactive oxidative metabolism and plays a crucial role in the antioxidant system in regulating the reduction/oxidation balance by scavenging reactive oxygen species, which is implicated in the mechanism of asthma. As for the mechanisms by which TRX exerts its beneficial effects, some studies have shown that TRX suppresses allergic inflammation in animal models of asthma. Recently, we reported that TRX directly modulated the chemotaxis of eosinophils, which have been shown to play a pivotal role in the mechanism of allergic airway inflammation, in the absence of T helper (Th)1 or Th2 cytokines. Further, serum TRX levels in patients with asthma were significantly increased in patients with attacks compared with those in the asymptomatic period. This review focuses on TRX in allergic reactions and discusses the physiological role of TRX.
Effect of honey, dextromethorphan, and no treatment on nocturnal cough and sleep quality for coughing children and their parents.

OBJECTIVES To compare the effects of a single nocturnal dose of buckwheat honey or honey-flavored dextromethorphan (DM) with no treatment on nocturnal cough and sleep difficulty associated with childhood upper respiratory tract infections. DESIGN A survey was administered to parents on 2 consecutive days, first on the day of presentation when no medication had been given the prior evening and then the next day when honey, honey-flavored DM, or no treatment had been given prior to bedtime according to a partially double-blinded randomization scheme. SETTING A single, outpatient, general pediatric practice. PARTICIPANTS One hundred five children aged 2 to 18 years with upper respiratory tract infections, nocturnal symptoms, and illness duration of 7 days or less. INTERVENTION A single dose of buckwheat honey, honey-flavored DM, or no treatment administered 30 minutes prior to bedtime. MAIN OUTCOME MEASURES Cough frequency, cough severity, bothersome nature of cough, and child and parent sleep quality. RESULTS Significant differences in symptom improvement were detected between treatment groups, with honey consistently scoring the best and no treatment scoring the worst. In paired comparisons, honey was significantly superior to no treatment for cough frequency and the combined score, but DM was not better than no treatment for any outcome. Comparison of honey with DM revealed no significant differences. CONCLUSIONS In a comparison of honey, DM, and no treatment, parents rated honey most favorably for symptomatic relief of their child's nocturnal cough and sleep difficulty due to upper respiratory tract infection. Honey may be a preferable treatment for the cough and sleep difficulty associated with childhood upper respiratory tract infection. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00127686.
Survival Trends and Long-Term Toxicity in Pediatric Patients with Osteosarcoma

Background. This study was conducted to investigate the clinical characteristics and treatment results of osteosarcoma in pediatric patients during the past 30 years. Trends in survival rates and long-term toxicity were analyzed. Procedure. 130 pediatric patients under the age of 20 years with primary localized or metastatic high-grade osteosarcoma were analyzed regarding demographic, treatment-related variables, long-term toxicity, and survival data. Results. Comparison of the different time periods of treatment showed that the 5-year OS improved from 58.6% for children diagnosed during 1979–1983 to 78.6% for those diagnosed during 2003–2008 (P = 0.13). Interestingly, the basic treatment agents including cisplatin, doxorubicin, and methotrexate remained the same. Treatment reduction due to acute toxicity was less frequent in patients treated in the last era (7.1% versus 24.1% in patients treated in 1979–1983; P = 0.04). Furthermore, late cardiac effects and secondary malignancies can become evident many years after treatment. Conclusion. We elucidate the prevalence of toxicity to therapy of patients with osteosarcoma over the past 30 years. The overall improvement in survival may in part be attributed to improved supportive care allowing regimens to be administered to best advantage with higher tolerance of chemotherapy and therefore less chemotherapy-related toxicity.
New Casbane Diterpenoids from a South China Sea Soft Coral, Sinularia sp

Six new casbane diterpenoids, named as sinularcasbanes A–F (1–6), along with six known analogues 7–12, were isolated from a South China Sea soft coral, Sinularia sp. The structures of the new compounds were elucidated by extensive spectroscopic analysis and by comparison with data reported in the literature. All compounds were evaluated for their cytotoxicity against selected cancer cell lines and the inhibition of lipopolysaccharide (LPS)-induced nitric oxide (NO) production in mouse peritoneal macrophages.