Miracle-dz/UniFAR-FTUs huggingface dataset:
Tumor necrosis factor: An updated review of its biology

Objective:To review the role of tumor necrosis factor (TNF) in the pathogenesis of the septic shock syndrome. Data Sources:The international English language literature from 1985 to present formed the basis for this review. MEDLINE was used to identify pertinent animal and human studies pertaining to the clinically relevant aspects of TNF and related cytokines. Study Selection: Those studies that focused on developments that may lead to advances in the therapy for septic shock syndrome were emphasized. Investigations that described in vivo and human results served as the primary database. Data Extraction: Animal studies were selected based on the similarity of the model pathogenesis and outcomes to the human clinical sepsis syndrome. Patient studies were selected on the basis of study design and sample size. Data Synthesis: The normal role of TNF and pathologic effects consequent to the excessive production of TNF in response to an overwhelming infection or injury are reviewed. Evidence establishes the role of TNF in septic shock syndrome. Novel therapies, such as anti-TNF monoclonal antibodies, soluble TNF receptors, or soluble TNF receptor-immunoglobulin G heavy chain fusion proteins, may confer protection against septic shock syndrome. Conclusions: TNF plays a major role in the pathogenesis of the septic shock syndrome. TNF exerts a range of beneficial and injurious effects that may ultimately lead to organ dysfunction and death. The burst of TNF release after endotoxemia promotes the progression of the shock syndrome even in the absence of further TNF release. New therapies targeted to the attenuation of TNF may hold promise for the management of patients with septic shock syndrome. (Crit Care Med 1993; 21:S415-S422)
A Pipeline Replica Bitline Technique for Suppressing Timing Variation of SRAM Sense Amplifiers in a 28-nm CMOS Process

With advances in semiconductor technology, the threshold voltage variation has worsened, which has a great impact on the speed and stability of static random access memory (SRAM). This paper proposes a pipeline replica bitline (RBL) delay technique designed to reduce the timing variation of SRAM sense amplifiers. This design takes full advantage of all cells in the RBL as replica cells (RCs). A tunable pipeline structure is applied to control the discharge of groups of RCs. The structure is designed based on theoretical analysis and fabricated using an SMIC 28-nm CMOS process. The measurement results show that the delay variation can be reduced by approximately 43% and 32% compared with the conventional RBL and multistage RBL, respectively. Furthermore, with slight tuning of the normal 28-nm foundry process, four wafers were obtained under extreme conditions to comprehensively test the proposed technique. The results show that the proposed technique is more stable than other techniques in any extreme condition.
VIPERdb: a relational database for structural virology

VIPERdb () is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry.
Dynamic-sized nonblocking hash tables

This paper presents nonblocking hash table algorithms that support resizing in both directions: shrinking and growing. The heart of the table is a freezable set abstraction, which greatly simplifies the task of moving elements among buckets during a resize. Furthermore, the freezable set abstraction makes possible the use of highly optimized implementations of individual buckets, including implementations in which a single flat array is used for each bucket, which improves cache locality. We present lock-free and wait-free variants of our hash table, to include fast adaptive wait-free variants based on the Fastpath/Slowpath methodology. In evaluation on SPARC and x86 architectures, we find that performance of our lock-free implementation is consistently better than the current state-of-the-art split-ordered list, and that performance for the adaptive wait-free algorithm is compelling across microbenchmark configurations.
Impact of bowel preparation on efficiency and cost of colonoscopy

OBJECTIVES:The impact of bowel preparation on the cost and efficiency of colonoscopy is uncertain. The aim of this study was to measure the impact of bowel preparation on total direct cost as well as procedure time and volume.METHODS:For 200 consecutive outpatient colonoscopies in persons with intact colons both at a private university hospital and at a public university hospital, we recorded the time spent suctioning fluid and feces from the colon and the time spent washing the colon to clean the mucosa. We prospectively asked colonoscopists to designate examinations that should be repeated at an interval sooner than would otherwise be recommended because of imperfect preparation. The data were used to perform a cost analysis of the economic effect of bowel preparation on direct costs of colonoscopy.RESULTS:Suctioning fluid and washing occupied 6% and 1.5% of total examination time (including insertion and withdrawal) at the public hospital and 9% and 1.3% at the private hospital. Patients at the public hospital were more likely to have an aborted examination (6.5% vs 1%, p = 0.004) and to be brought back earlier than suggested or required by current practice standards because of imperfect bowel preparation (20% vs 12.5%, p = 0.04). Cost analysis indicated that to complete the initial examinations and the first round of surveillance, imperfect bowel preparation resulted in a 12% increase in costs at the university hospital and a 22% increase at the public hospital.CONCLUSIONS:The increase in colonoscopy costs associated with imperfect preparation is substantial, and seems likely to vary among practices. Aborted examinations and surveillance examinations performed earlier than recommended because of imperfect preparation are appropriate targets for continuous quality improvement programs. More reliable bowel preparations, or measures to improve patient compliance with bowel preparation, could significantly reduce the costs of colonoscopy in clinical practice.
Dendritic Architecture of Principal Basolateral Amygdala Neurons Changes Congruently with Endocrine Response to Stress

Animals cope with changing environments through changes in behavior. Such plasticity is, however, marked by substantial inter-individual variability. Neuroendocrine reactivity to challenging environments can be an important predictor of resilience. Both basolateral amygdala (BLA) neurons and adrenal glucocorticoid signaling are integral parts of the stress neuroendocrine response. In this report, we test if individual variation in hormonal response to stress is associated with individual variation in the dendritic complexity of BLA neurons. We report a positive correlation between inter-individual variability in glucocorticoid response and neuronal plasticity in the BLA subsequent to a stressor. This suggests that stressful experiences in the past act as significant sculptors of BLA neuronal plasticity and congruent neuroendocrine response.
Finite-SNR regime analysis of the Gaussian wiretap multiple-access channel

In this work, we consider a K-user Gaussian wiretap multiple-access channel (GW-MAC) in which each transmitter has an independent confidential message for the receiver. There is also an external eavesdropper who intercepts the communications. The goal is to transmit the messages reliably while keeping them confidential from the eavesdropper. To accomplish this goal, two different approaches have been proposed in prior works, namely, i.i. d. Gaussian random coding and real alignment. However, the former approach fails at moderate and high SNR regimes as its achievable result does not grow with SNR. On the other hand, while the latter approach gives a promising result at the infinite SNR regime, its extension to the finite-SNR regime is a challenging task. To fill the gap between the performance of the existing approaches, in this work, we establish a new scheme in which, at the receiver's side, it utilizes an extension of the compute-and-forward decoding strategy and at the transmitters' side it exploits lattice alignment, cooperative jamming, and i.i. d. random codes. For the proposed scheme, we derive a new achievable bound on sum secure rate which scales with log(SNR) and hence it outperforms the i.i. d. Gaussian codes in moderate and high SNR regimes. We evaluate the performance of our scheme, both theoretically and numerically. Furthermore, we show that our sum secure rate achieves the optimal sum secure degrees of freedom in the infinite-SNR regime.
Regulation of gene expression in flux balance models of metabolism.

Genome-scale metabolic networks can now be reconstructed based on annotated genomic data augmented with biochemical and physiological information about the organism. Mathematical analysis can be performed to assess the capabilities of these reconstructed networks. The constraints-based framework, with flux balance analysis (FBA), has been used successfully to predict time course of growth and by-product secretion, effects of mutation and knock-outs, and gene expression profiles. However, FBA leads to incorrect predictions in situations where regulatory effects are a dominant influence on the behavior of the organism. Thus, there is a need to include regulatory events within FBA to broaden its scope and predictive capabilities. Here we represent transcriptional regulatory events as time-dependent constraints on the capabilities of a reconstructed metabolic network to further constrain the space of possible network functions. Using a simplified metabolic/regulatory network, growth is simulated under various conditions to illustrate systemic effects such as catabolite repression, the aerobic/anaerobic diauxic shift and amino acid biosynthesis pathway repression. The incorporation of transcriptional regulatory events in FBA enables us to interpret, analyse and predict the effects of transcriptional regulation on cellular metabolism at the systemic level.
A 1400-Year Bølling-Allerød Tree-Ring Record from the U.S. Great Lakes Region

Abstract Since the late 19th Century, geologists and naturalists working in the US Midwest have reported an abundance of tree macrofossils embedded in glacial and lacustrine deposits formed after the Last Glacial Maximum. The most widely-known of these sites is the Two Creeks type locality in Wisconsin. We report progress on development of a long tree-ring record from this subfossil wood in the US Great Lakes region, employing samples collected during a decade-long series of field campaigns at recently eroded lake shorelines, construction projects, and excavations, along with acquisition of archived samples collected from the 1950s to the 1980s during past lake erosion events. A previously-reported tree-ring chronology from the Two Creeks type locality reached ca. 250 years in length; here we used radiocarbon dates and tree-ring crossdating to develop a 1408-year tree-ring chronology (mainly spruce [Picea spp.] with some tamarack [Larix]) comprising a total of 135 overlapped tree-ring width series in three clusters from nine locations in eastern Wisconsin. The calendar age of the record is estimated with 46 14C dates to between 14,500 to 13,100 cal BP. This is currently the oldest and only long tree-ring record in North America from the boreal environments of the Bølling-Allerød warm period during the transition from the Late Glacial to the Holocene.
Hemispherectomy for intractable epilepsy in adults: The first reported series

Hemispherectomy for intractable unihemispheric epilepsy (IUE) has long been established in pediatric patients. This study reports the first series examining hemispherectomy exclusively in adult patients (>18 years old). Nine adults with IUE underwent hemispherectomy at the University of Minnesota. All patients had unilateral hemiplegia and visual field loss. Seven patients (77.8%) were Engel class I/II at last follow‐up. Five (83.3%) of the six patients with >30 years of follow‐up were seizure free. No surgery‐related mortality, hydrocephalus, or superficial cerebral hemosiderosis occurred. Hemispherectomy is an effective procedure in appropriately selected adult patients, resulting in excellent long‐term seizure control and no mortality. Ann Neurol 2007
The differential clinical and neurocognitive profiles of COMT SNP rs165599 genotypes in schizophrenia

Schizophrenia is characterized by profound disturbances in cognition, emotion, and social functioning. Catechol-O-methyl transferase (COMT) is the important enzyme for the metabolism of monoamines, which play important part in the pathogenesis of schizophrenia. COMT exists in high and low activity forms. The low activity form was found to be an amino acid substitution (Val-108-Met), which reduces the thermostability of the enzyme. This genetic polymorphism has been reported to be associated with schizophrenia and its associated clinical features (Li et al., 1996).
The Impact of Video Transcoding Parameters on Event Detection for Surveillance Systems

The process of transcoding videos apart from being computationally intensive, can also be a rather complex procedure. The complexity refers to the choice of appropriate parameters for the transcoding engine, with the aim of decreasing video sizes, transcoding times and network bandwidth without degrading video quality beyond some threshold that event detectors lose their accuracy. This paper explains the need for transcoding, and then studies different video quality metrics. Commonly used algorithms for motion and person detection are briefly described, with emphasis in investigating the optimum transcoding configuration parameters. The analysis of the experimental results reveals that the existing video quality metrics are not suitable for automated systems and that the detection of persons is affected by the reduction of bit rate and resolution, while motion detection is more sensitive to frame rate.
Distribution of Elements/Parameters in Agricultural and Grazing Land Soil of Europe

The GEMAS maps provide useful harmonised data for regional-scale bedrock (parent material) geochemical mapping and contribute to the geologist's knowledge about the average composition of the UCC. The GEMAS data are needed for evidence-based political decision-making in Europe. Apart from staisfying the EU REACH regulation on the chemical composition agricultural and grazing land soil, they will find applications in forensic science, medical geology, mineral exploration, and in further wide-ranging academic research. They can also be used as a data set for ground-thruting of remotely-sensed satellite observations that relate to soil composition. Last, but not least, they provide the farming community with a comparative database about soil quality, fertillity and the impact of certain farming practices at the European scale.
Conference Scene: Environmental epigenomics and disease susceptibility

The main objective of this conference was to provide solid evidence that environmental exposures during early development can affect faithful reproduction of individual parental epigenomes without changing DNA sequence in the offspring. No doubt, this important goal has been successfully achieved owing to the high quality of presented epidemiological and experimental studies and engaging discussions of many yet to be published results. Compelling data suggested a strong causal link between prenatal vulnerability of future parental epigenomes to damaging environmental factors aggravated by abnormal socio-cultural conditions (including, for instance, malnutrition and chronic stress) and the alarming risk of developing heritable complex medical conditions later in life, such as asthma, autism, cancer, cardiovascular disease, diabetes, obesity, schizophrenia and a whole range of rare neuromuscular pathologies. It was concluded that modern epigenetic research promises to markedly improve our ability to diagnos.
Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions.

The solution structure of the oligodeoxynucleotide 5'-d(CTCGGCXCCATC)-3'. 5'-d(GATGGCGCCGAG)-3' containing the heterocyclic amine 8-[(3-methyl-3H-imidazo[4,5-f]quinolin-2-yl)amino]-2'-deoxyguanosine adduct (IQ) at the third guanine in the NarI restriction sequence, a hot spot for -2 bp frameshifts, is reported. Molecular dynamics calculations restrained by distances derived from 24 (1)H NOEs between IQ and DNA, and torsion angles derived from (3)J couplings, yielded ensembles of structures in which the adducted guanine was displaced into the major groove with its glycosyl torsion angle in the syn conformation. One proton of its exocyclic amine was approximately 2.8 A from an oxygen of the 5' phosphodiester linkage, suggesting formation of a hydrogen bond. The carcinogen-guanine linkage was defined by torsion angles alpha' [N9-C8-N(IQ)-C2(IQ)] of 159 +/- 7 degrees and beta' [C8-N(IQ)-C2(IQ)-N3(IQ)] of -23 +/- 8 degrees . The complementary cytosine was also displaced into the major groove. This allowed IQ to intercalate between the flanking C.G base pairs. The disruption of Watson-Crick hydrogen bonding was corroborated by chemical-shift perturbations for base aromatic protons in the complementary strand opposite to the modified guanine. Chemical-shift perturbations were also observed for (31)P resonances corresponding to phosphodiester linkages flanking the adduct. The results confirmed that IQ adopted a base-displaced intercalated conformation in this sequence context but did not corroborate the formation of a hydrogen bond between the IQ quinoline nitrogen and the complementary dC [Elmquist, C. E. ; Stover, J. S. ; Wang, Z. ; Rizzo, C. J. J. Am. Chem. Soc. 2004, 126, 11189-11201].
Long-term exposure to outdoor air pollution and the incidence of chronic obstructive pulmonary disease in a national English cohort

Objectives The role of outdoor air pollution in the incidence of chronic obstructive pulmonary disease (COPD) remains unclear. We investigated this question using a large, nationally representative cohort based on primary care records linked to hospital admissions. Methods A cohort of 812 063 patients aged 40–89 years registered with 205 English general practices in 2002 without a COPD diagnosis was followed from 2003 to 2007. First COPD diagnoses recorded either by a general practitioner (GP) or on admission to hospital were identified. Annual average concentrations in 2002 for particulate matter with an aerodynamic diameter <10 µm (PM10) and <2.5 µm (PM2.5), nitrogen dioxide (NO2), ozone and sulfur dioxide (SO2) at 1 km2 resolution were estimated from emission-based dispersion models. Hazard ratios (HRs) per interquartile range change were estimated from Cox models adjusting for age, sex, smoking, body mass index and area-level deprivation. Results 16 034 participants (1.92%) received a COPD diagnosis from their GP and 2910 participants (0.35%) were admitted to hospital for COPD. After adjustment, HRs for GP recorded COPD and PM10, PM2.5 and NO2 were close to unity, positive for SO2 (HR=1.07 (95% CI 1.03 to 1.11) per 2.2 µg/m3) and negative for ozone (HR=0.94 (0.89 to 1.00) per 3 µg/m3). For admissions HRs for PM2.5 and NO2 remained positive (HRs=1.05 (0.98 to 1.13) and 1.06 (0.98 to 1.15) per 1.9 µg/m3 and 10.7 µg/m3, respectively). Conclusions This large population-based cohort study found limited, inconclusive evidence for associations between air pollution and COPD incidence. Further work, utilising improved estimates of air pollution over time and enhanced socioeconomic indicators, is required to clarify the association between air pollution and COPD incidence.
Preoperative platelet response to collagen is associated with myocardial injury after off-pump coronary bypass graft in patients taking aspirin

Background We hypothesized that, even in patients taking aspirin, the variance of preoperative platelet response to collagen might be associated with myocardial injury during coronary artery bypass graft (CABG) surgery. Therefore, we evaluated the relationship between preoperative whole-blood aggregometry (WBA) by collagen and the postoperative myocardial injuries. Methods For 44 patients who were scheduled for elective off-pump CABG and taking aspirin, WBA was measured by the impedance method in the presence of collagen (2 mg/ml or 5 mg/ml) as stimulatory agents. After CABG, myocardial injury was evaluated by analysis of the creatine kinase (CK), creatine kinase-MB (CK-MB), and lactate dehydrogenase (LD), and by electrocardiography. Results High response group (n = 13) on preoperative WBA with collagen (2 and 5 mg/ml) showed significantly higher postoperative cardiac enzyme levels (CK, CK-MB and LD) than those of low response group (n = 31). Conclusions In patients who take aspirin and undergoing off-pump CABG, the preoperative platelet response to collagen is correlated with postoperative myocardial injury.
Knowledge Management and Musical Metadata

The explosion of digital music has created in the recent years an urgent need for powerful knowledge management techniques and tools. Without such tools, users are confronted to huge music catalogues they cannot fully exploit. The very nature of music calls for the development of specific knowledge management techniques: on the one hand, the goals of users are ill-defined, or rather, based on enjoyment rather than on clear tasks or problems to solve. On the other hand, music in Western countries has been the subject of a long tradition of formalization and knowledge which is of crucial importance for building reasonable music information systems. The article outlines the main issues on music management, and focuses on the three main types of musical metadata being currently considered: editorial, cultural and acoustic. For each of these, the main issues are stated and the most successful techniques are discussed.
A service-oriented architecture for billing resources in IaaS cloud platforms

Cloud Computing is a recent paradigm where different IT resources, such as applications or hardware, are quickly provisioned to customers through a pay per use model. Many research studies have already been conducted concerning billing services for cloud computing, but they lack on flexibility to establish how resources are defined and monitored. In fact, current solutions seem also very dependent on specific cloud infrastructures. This paper proposes an architecture for billing cloud services decoupled from specific providers, named as aCCountS. This service is complemented by a Domain Specific Language that allows the specification of flexible pricing policies. Such policies aims at supporting cloud billing requirements collected from our literature survey, allowing pricing schemes that meet different customer profiles. Based on this architecture, a prototype has been implemented and tested to validate our proposal in two different cloud infrastructures. Experiments confirmed that (i) the architecture hasn't dependencies of specific IaaS provider and (ii) the charging procedures are done correctly.