LLukas22/scidocs huggingface dataset:
Next generation sequencing of Cytokeratin 20-negative Merkel cell carcinoma reveals ultraviolet-signature mutations and recurrent TP53 and RB1 inactivation

Merkel cell carcinoma is a rare but highly aggressive cutaneous neuroendocrine carcinoma. Cytokeratin 20 (CK20) is expressed in ~95% of Merkel cell carcinomas and is useful for distinction from morphologically similar entities including metastatic small-cell lung carcinoma. Lack of CK20 expression may make diagnosis of Merkel cell carcinoma more challenging, and has unknown biological significance. Approximately 80% of CK20-positive Merkel cell carcinomas are associated with the oncogenic Merkel cell polyomavirus. Merkel cell carcinomas lacking Merkel cell polyomavirus display distinct genetic changes from Merkel cell polyomavirus-positive Merkel cell carcinoma, including RB1 inactivating mutations. Unlike CK20-positive Merkel cell carcinoma, the majority of CK20-negative Merkel cell carcinomas are Merkel cell polyomavirus-negative, suggesting CK20-negative Merkel cell carcinomas predominantly arise through virus-independent pathway(s) and may harbor additional genetic differences from conventional Merkel cell carcinoma. Hence, we analyzed 15 CK20-negative Merkel cell carcinoma tumors (10 Merkel cell polyomavirus-negative, four Merkel cell polyomavirus-positive, and one undetermined) using the Ion Ampliseq Comprehensive Cancer Panel, which assesses copy number alterations and mutations in 409 cancer-relevant genes. Twelve tumors displayed prioritized high-level chromosomal gains or losses (average 1.9 per tumor). Non-synonymous high-confidence somatic mutations were detected in 14 tumors (average 11.9 per tumor). Assessing all somatic coding mutations, an ultraviolet-signature mutational profile was present, and more prevalent in Merkel cell polyomavirus-negative tumors. Recurrent deleterious tumor suppressor mutations affected TP53 (9/15, 60%), RB1 (3/15, 20%), and BAP1 (2/15, 13%). Oncogenic activating mutations included PIK3CA (3/15, 20%), AKT1 (1/15, 7%) and EZH2 (1/15, 7%). In conclusion, CK20-negative Merkel cell carcinoma display overlapping genetic changes with CK20-positive Merkel cell carcinoma, including RB1 mutations restricted to Merkel cell polyomavirus-negative tumors. However, some CK20-negative Merkel cell carcinomas harbor mutations not previously described in Merkel cell carcinoma. Hence, CK20-negative Merkel cell carcinomas harbor diverse oncogenic drivers which may represent therapeutic targets in individual tumors.
Medicine prices , availability , and affordability in Vietnam

Objective: To assess the price, availability and affordability of a sample of medicines in Vietnam. Methods: Data on the price and availability of 42 medicines were collected using the standard World Health Organization/Health Action International (WHO/HAI) methodology in five geographical areas in Vietnam. The median price of these medicines was compared with the Management Science for Health international reference prices (IRPs), expressed as median price ratios. Affordability was measured as the number of days’ wages required for the lowest-paid unskilled government worker to purchase one course of therapy. Of the 42 medicines studied, 15 were chosen for international comparison, which were included in at least 80% of other country surveys using the WHO/HAI methodology. Results: Public sector availability of generic medicines was 33.6%. The median public procurement price was 1.82 times the IRPs for generics, but for some individual medicines it was less than half the IRP. The price to patients in public outlets was higher than in private pharmacies. Adjusted for Purchasing Power Parity in 2005, the lowest generic prices in private pharmacies were still 8.3 times the IRPs. Treatments were thus unaffordable for a large part of Vietnam’s population. Conclusions: Medicines in Vietnam were high in price, and low in both availability and affordability, especially in the public sector. To make public facilities a primary treatment option for the poor, Vietnam must reduce medicine prices in this sector by improving procurement efficiency, ensuring and promoting low-priced generics, and regulating reasonable mark-ups.
The Equivariant Tamagawa Number Conjecture : A survey

We give a survey of the equivariant Tamagawa number (a.k.a. Bloch-Kato) conjecture with particular emphasis on proven cases. The only new result is a proof of the 2-primary part of this conjecture for Tate-motives over abelian fields. This article is an expanded version of a survey talk given at the conference on Stark’s conjecture, Johns Hopkins University, Baltimore, August 5-9, 2002. We have tried to retain the succinctness of the talk when covering generalities but have considerably expanded the section on examples. Most of the following recapitulates well known material due to many people. Section 3 is joint work with D. Burns (for which [14], [15], [16], [17] are the main references). In section 5.1 we have given a detailed proof of the main result which also covers the prime l = 2 (unavailable in the literature so far).
Effects of cognitive stimulation therapy Japanese version (CST-J) for people with dementia: a single-blind, controlled clinical trial

OBJECTIVES
Cognitive stimulation therapy (CST) has shown to have significant benefits in improving the cognitive function and quality of life (QOL) in people with mild-to-moderate dementia in a UK randomized controlled trial (RCT). We developed and examined the Japanese version of group CST (CST-J) in a single-blind, controlled clinical trial.


METHOD
CST-J consisting of 14 sessions was administered to a treatment group (n = 26) twice a week for 7 weeks. The treatment group was compared with a control group (n = 30). Based on single-blindness, cognition was evaluated by a researcher, and QOL and mood were rated by the participants themselves. Additionally, QOL and mood of participants were rated by care workers who were not blind but who observed them most directly in their daily life (important for social validity).


RESULTS
A linear mixed model was used for analyses of cognition and QOL. There were significant improvements in cognition [COGNISTAT (Neurobehavioral Cognitive Status Examination) and MMSE (Mini-Mental State Examination)] for the treatment group compared with the control group (p < 0.01). Regarding QOL, the EQ-5D was significant (p = 0.019) and the QoL-AD (Quality of Life - Alzheimer's Disease) showed a positive trend (p = 0.06) when rated by care workers, although not when rated by the participants themselves. Using a nonparametrical analysis, there were significant improvements in the face scale for mood when rated by both the participants (p < 0.01) and the care workers (p = 0.017).


CONCLUSION
The CST-J shows promising improvements in cognition, mood, and aspects of QOL for people with dementia in Japanese care settings. A large RCT is now needed.
The Wikipedia Corpus

Wikipedia, the popular online encyclopedia, has in just six years grown from an adjunct to the now-defunct Nupedia to over 31 million pages and 429 million revisions in 256 languages and spawned sister projects such as Wiktionary and Wikisource. Available under the GNU Free Documentation License, it is an extraordinarily large corpus with broad scope and constant updates. Its articles are largely consistent in structure and organized into category hierarchies. However, the wiki method of collaborative editing creates challenges that must be addressed. Wikipedia’s accuracy is frequently questioned, and systemic bias means that quality and coverage are uneven, while even the variety of English dialects juxtaposed can sabotage the unwary with differences in semantics, diction and spelling. This paper examines Wikipedia from a research perspective, providing basic background knowledge and an understanding of its strengths and weaknesses. We also solve a technical challenge posed by the enormity of text (1.04TB for the English version) made available with a simple, easily-implemented dictionary compression algorithm that permits time-efficient random access to the data with a twenty-eight-fold reduction in size.
Left Ventricular Reverse Remodeling With Biventricular Versus Right Ventricular Pacing in Patients With Atrioventricular Block and Heart Failure in the BLOCK HF Trial.

BACKGROUND
Biventricular pacing in heart failure (HF) improves survival, relieves symptoms, and attenuates left ventricular (LV) remodeling. However, little is known about biventricular pacing in HF patients with atrioventricular block because they are typically excluded from biventricular trials.


METHODS AND RESULTS
The Biventricular versus Right Ventricular Pacing in Heart Failure Patients with Atrioventricular Block (BLOCK HF) trial randomized patients with atrioventricular block, New York Heart Association symptom classes I to III HF, and LV ejection fraction ≤50% to biventricular or right ventricular pacing. Doppler echocardiograms were obtained at randomization (after 30 to 60 days of right ventricular pacing postimplant) and every 6 months through 24 months. Data analysis comparing changes in 10 prespecified echo parameters over time was conducted using a Bayesian design. LV end systolic volume index was also evaluated as a predictor of mortality/morbidity. Of 691 randomized subjects, 624 had paired Doppler echocardiogram data for ≥1 analyses at 6, 12, 18, or 24 months. Biventricular pacing significantly reduced LV volume indices and intraventricular mechanical delay, and improved LV ejection fraction, consistent with LV reverse remodeling. These parameters showed little change with right ventricular pacing alone, indicating no systematic reverse remodeling with right ventricular pacing. LV end systolic volume index was predictive of mortality/morbidity; the estimated risk increased up to 1% for every 1 mL/m(2) increase in LV end systolic volume index.


CONCLUSIONS
LV end systolic volume index is a significant predictor of mortality/morbidity in this population. Cardiac structure and function are improved with biventricular pacing for patients with atrioventricular block and LV systolic dysfunction.


CLINICAL TRIAL REGISTRATION
URL: http://www.clinicaltrials.gov. Unique identifier: NCT00267098.
Detection of Opinion Spam with Character n-grams

In this paper we consider the detection of opinion spam as a stylistic classification task because, given a particular domain, the deceptive and truthful opinions are similar in content but differ in the way opinions are written (style). Particularly, we propose using character ngrams as features since they have shown to capture lexical content as well as stylistic information. We evaluated our approach on a standard corpus composed of 1600 hotel reviews, considering positive and negative reviews. We compared the results obtained with character n-grams against the ones with word n-grams. Moreover, we evaluated the effectiveness of character n-grams decreasing the training set size in order to simulate real training conditions. The results obtained show that character n-grams are good features for the detection of opinion spam; they seem to be able to capture better than word n-grams the content of deceptive opinions and the writing style of the deceiver. In particular, results show an improvement of 2.3% and 2.1% over the word-based representations in the detection of positive and negative deceptive opinions respectively. Furthermore, character n-grams allow to obtain a good performance also with a very small training corpus. Using only 25% of the training set, a Näıve Bayes classifier showed F1 values up to 0.80 for both opinion polarities.
ptimal Timing for the Initiation of reTreatment With 300 mg Clopidogrel efore Percutaneous Coronary Intervention

OBJECTIVES This study sought to determine the optimal timing of a 300-mg clopidogrel loading dose before percutaneous coronary intervention (PCI) in patients enrolled in the Clopidogrel for the Reduction of Events During Observation (CREDO) trial. BACKGROUND A loading dose of clopidogrel before a PCI has become relatively commonplace, although the data supporting this practice are limited and sometimes conflicting. METHODS Patients were randomized to receive either 300 mg clopidogrel or a matching placebo administered a minimum of 3 h and a maximum of 24 h before PCI. The primary 28-day combined end point was death, myocardial infarction, or urgent target vessel revascularization. Linear splines were used to summarize the effect of the time of pre-treatment as a continuous variable. RESULTS A total of 1,762 patients were evaluated. For patients randomized to placebo, there was no relationship between the duration of pre-treatment and the occurrence of the primary end point, whereas longer durations of pre-treatment in patients randomized to clopidogrel were associated with improved outcomes. The event rates diverged maximally at 24 h. The difference in outcomes between placebo and clopidogrel pre-treated patients was not significant until 15 h pre-treatment, with a 58.8% (p 0.028) reduction in the primary end point in patients pre-treated with clopidogrel 15 h compared with placebo. CONCLUSIONS When a 300-mg loading dose of clopidogrel is used, little benefit is obtained compared with just 75 mg at the time of the PCI when the treatment duration is 12 h. In patients pre-treated for longer durations, the optimal duration seems to approach 24 h. (J Am Coll ublished by Elsevier Inc. doi:10.1016/j.jacc.2005.10.047
Effects of different PHEV control strategies on vehicle performance

Foreign oil dependence, increased cost of fuel, pollution, global warming are buzz words of today's era. Automobiles have a large impact on increasing energy demand, pollution and related issues. As a consequence, many efforts are being concentrated on innovative systems for transportation that could replace petroleum with cleaner fuel, i.e. electricity from the power grid. The use of plug-in hybrid electric vehicles (PHEVs) can become a very important change in this direction, since such vehicles could benefit from the increasing availability of renewable energy. PHEVs requires new control and energy management algorithms, that are crucial for vehicle performance. This paper deals with evaluation of two modes, Electric Vehicle (EV) mode and Blended mode, for plug-in hybrid electric vehicles and their comparison with conventional and hybrid electric vehicle performance.
Preferential {100} grain orientation in 10 micrometer-thick laser crystallized multicrystalline silicon on glass

Abstract Liquid phase crystallization of 10 μm thin silicon layers on glass substrates was performed with a line-shaped continuous wave laser beam. The process window was investigated in terms of the scanning velocity of the laser, the pre-heating of the specimens and the applied laser intensity. We have identified the entire process window, in which large-scale crystallization without deformation or destruction of the substrate and cracking of the silicon layer can be obtained. The grain orientations of the resulting Si layers were analyzed using both electron backscatter diffraction (EBSD) and X-ray diffraction (XRD). The influence of the critical crystallization parameters on the grain orientation of the silicon film was examined. EBSD and XRD measurements show that a preferential {100} surface texture and {100} and {101} orientations in scanning direction of the laser can be achieved if appropriate crystallization parameters are used. This texture formation is accompanied with a substantial decrease of high angle grain boundaries.
Is planned vaginal delivery for breech presentation at term still an option? Results of an observational prospective survey in France and Belgium.

OBJECTIVE
A large trial published in 2000 concluded that planned vaginal delivery of term breech births is associated with high neonatal risks. Because the obstetric practices in that study differed from those in countries where planned vaginal delivery is still common, we conducted an observational prospective study to describe neonatal outcome according to the planned mode of delivery for term breech births in 2 such countries.


STUDY DESIGN
Observational prospective study with an intent-to-treat analysis to compare the groups for which cesarean and vaginal deliveries were planned. Associations between the outcome and planned mode of delivery were controlled for confounding by multivariate analysis. The main outcome measure was a variable that combined fetal and neonatal mortality and severe neonatal morbidity. The study population consisted of 8105 pregnant women delivering singleton fetuses in breech presentation at term in 138 French and 36 Belgian maternity units.


RESULTS
Cesarean delivery was planned for 5579 women (68.8%) and vaginal delivery for 2526 (31.2%). Of the women with planned vaginal deliveries, 1796 delivered vaginally (71.0%). The rate of the combined neonatal outcome measure was low in the overall population (1.59%; 95% CI [1.33-1.89]) and in the planned vaginal delivery group (1.60%; 95% CI [1.14-2.17]). It did not differ significantly between the planned vaginal and cesarean delivery groups (unadjusted odds ratio = 1.10, 95% CI [0.75-1.61]), even after controlling for confounding variables (adjusted odds ratio = 1.40, 95% CI [0.89-2.23]).


CONCLUSION
In places where planned vaginal delivery is a common practice and when strict criteria are met before and during labor, planned vaginal delivery of singleton fetuses in breech presentation at term remains a safe option that can be offered to women.
Reducing the harm of opioid overdose with the safe use of naloxone : a pharmacologic review.

INTRODUCTION
Opioid overdose fatality has increased threefold since 1999. As a result, prescription drug overdose surpassed motor vehicle collision as the leading cause of unintentional injury-related death in the USA. Naloxone , an opioid antagonist that has been available for decades, can safely reverse opioid overdose if used promptly and correctly. However, clinicians often overestimate the dose of naloxone needed to achieve the desired clinical outcome, precipitating acute opioid withdrawal syndrome (OWS).


AREAS COVERED
This article provides a comprehensive review of naloxone's pharmacologic properties and its clinical application to promote the safe use of naloxone in acute management of opioid intoxication and to mitigate the risk of precipitated OWS. Available clinical data on opioid-receptor kinetics that influence the reversal of opioid agonism by naloxone are discussed. Additionally, the legal and social barriers to take home naloxone programs are addressed.


EXPERT OPINION
Naloxone is an intrinsically safe drug, and may be administered in large doses with minimal clinical effect in non-opioid-dependent patients. However, when administered to opioid-dependent patients, naloxone can result in acute opioid withdrawal. Therefore, it is prudent to use low-dose naloxone (0.04 mg) with appropriate titration to reverse ventilatory depression in this population.
Insomnia disorder

Insomnia disorder affects a large proportion of the population on a situational, recurrent or chronic basis and is among the most common complaints in medical practice. The disorder is predominantly characterized by dissatisfaction with sleep duration or quality and difficulties initiating or maintaining sleep, along with substantial distress and impairments of daytime functioning. It can present as the chief complaint or, more often, co-occurs with other medical or psychiatric disorders, such as pain and depression. Persistent insomnia has been linked with adverse long-term health outcomes, including diminished quality of life and physical and psychological morbidity. Despite its high prevalence and burden, the aetiology and pathophysiology of insomnia is poorly understood. In the past decade, important changes in classification and diagnostic paradigms have instigated a move from a purely symptom-based conceptualization to the recognition of insomnia as a disorder in its own right. These changes have been paralleled by key advances in therapy, with generic pharmacological and psychological interventions being increasingly replaced by approaches that have sleep-specific and insomnia-specific therapeutic targets. Psychological and pharmacological therapies effectively reduce the time it takes to fall asleep and the time spent awake after sleep onset, and produce a modest increase in total sleep time; these are outcomes that correlate with improvements in daytime functioning. Despite this progress, several challenges remain, including the need to improve our knowledge of the mechanisms that underlie insomnia and to develop more cost-effective, efficient and accessible therapies.
Sexual function in pre- and post-menopausal women with obstructive sleep apnea syndrome

The objective of this study was to evaluate the female sexual function in relation to hormonal status in pre- and postmenopausal women with obstructive sleep apnea (OSA). A total of 43 premenopausal (mean age 42.1±4.9) and 58 postmenopausal (mean age 59.9±4.8) women were included in the study. All women filled out the Epworth sleepiness scale (ESS), the Beck Depression Inventory (BDI) and the Female Sexual Function Index (FSFI). Testosterone, estradiol and progesterone were measured. After polysomnography, women were allocated to a not-severe OSA group (Apnea–Hypopnea Index (AHI) 10–30) and a severe OSA group (AHI >30). Healthy subjects comprised the control group. Severe OSA women in both pre- and post-menopausal group were found to have significantly lower mean FSFI score (16.5±4.0 and 16.9±4.7, respectively) compared with not-severe OSA (23.4±5.5, P<0.01 and 21.8±7.5, P<0.05) and control subjects (27.0±5.5, P<0.01 and 24.0±6.7, P<0.01). Progesterone, which was significantly lower in severe OSA premenopausal women (0.26±0.2) compared with not-severe OSA (0.55±0.14, P<0.01) and control group (0.62±0.16, P<0.01), correlated significantly with FSFI (r=0.39, P<0.01). Our study demonstrated that OSA is associated with sexual dysfunction in both premenopausal and postmenopausal women in a dose-related fashion. Regarding premenopausal women, our results indicated that progesterone may play a role in the association between OSA and female sexual dysfunction.
The discontent degree in relations with the proximal social environment and adolescent personality features in Timis County, Romania.

UNLABELLED
In our study we investigated whether there is a relation between the degree of discontent in relations with the proximal social environment (family and peer groups) and adolescent personality features. The study was conducted on a statistical representative and homogenous sample consisting of 2908 teenagers (51.5% girls and 48.5 % boys, aged between 15 and 19 years). It was an observational (case) study and it consisted in 2 questionnaires applying: Freiburg Personality Inventory (212 items) and CORT 2004 questionnaire (116 items, 6 referring to the discontent levels created by proximal social environment). Cronbach's alpha index was 0.802 for FPI and 0,910 for CORT 2004. Statistical analysis was performed by SPSS 16 program applying Chi square (χ2) and gamma (γ) correlation.


RESULTS
Depression and Emotional lability correlated positively and powerfully with q15 (discontent degree of relations with present friend-peers) (γ = 0.471, Sig. 0.000, and γ = 0.383, Sig. 0.000, respectively) and q5 (discontent degree of the relation with parents) (γ = 0.380, Sig. 0.000, and γ = 0.337, Sig. 0.000, respectively). Sociability and calm correlated negative with q5 (γ = -0.14, Sig. 0.000, and γ = -0.35, Sig. 0.000, respectively), q15 (γ = -0.33, Sig. 000 and γ = -0.18, Sig. 000, respectively). In conclusion, there is direct proportional relation between the discontent degree of relations with friend-peers and parents and depression and emotional lability, and inverse proportional relation of friend-peers and parents with sociability and calm.