Miracle-dz/UniFAR-FTUs huggingface dataset:
Ageing research in the post-genome era: new technologies for an old problem.

The sequencing of a growing number of genomes, and of the human genome in particular, has paved the way for remarkable technological innovations that are revolutionizing research across the life sciences. Large-scale sequencing and emerging techniques and approaches, like microarrays and systems biology, are changing the way researchers study life and its intrinsic complexity. Cells and the molecules that compose them, in particular proteins programmed from the genome to give rise to complex interactions and functions, can now be studied in a high-throughput fashion. Genomics and its derivative technologies promise to transform biomedical research and be the preeminent area of scientific discovery during the 21st century. New technologies are particularly useful in scientific fields that have already been the subject of considerable research, and thus for which substantial observations exist, but that remain largely unsolved (de Magalhães and Toussaint, 2004a). Biogerontology is one of such fields and the post-genome era promises to be a time of unprecedented breakthroughs in our understanding of ageing. The goal of this chapter is to review some of the key technological and methodological advances made possible by the recent sequencing of genomes and summarize their relevance to the study of complex traits like longevity, ageing and age-related diseases.
Title Influence of antimicrobial regimen on decreased in-hospital mortality ofpatients with MRSA bacteremia

1 Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important 2 causes of bacteremia. Recently, several epidemiological and microbiological changes have 3 become evident in MRSA infections. The purposes of this study were to assess clinical 4 characteristics of patients with MRSA bacteremia and microbiological changes in MRSA. 5 We conducted a retrospective observational study on patients with MRSA bacteremia who 6 were hospitalized between 2008 and 2011. We used univariate and multivariate analysis to 7 evaluate the predictors associated with 30-day mortality. The 7-day and 30-day mortality 8 rates were 12.0% and 25.3%, respectively. According to multivariate analysis, the 9 independent predictors that associated with 30-day mortality were leukopenia, low serum 10 albumin, high sequential organ failure assessment (SOFA) score, and quinolone use within 30 11 days. Compared to previous data (2003–2007), the SOFA score of the new data set remained 12 unchanged, but in-hospital mortality decreased significantly. In particular, the mortality 13 associated with use of vancomycin (VCM) was significantly lower. Although the minimum 14 inhibitory concentration of VCM required to inhibit the growth of 90% of organisms (MIC90) 15 had not changed, the trough value of VCM changed significantly; a VCM trough value of 10 16 or greater was significantly higher compared to previous data. Of the staphylococcal cassette 17 chromosome mec (SCCmec) types, SCCmec II values decreased significantly, and SCCmec I 18 and IV values increased significantly. Our results indicate that changes in VCM usage might 19 contribute to decreased in-hospital mortality. 20 21
Early serum creatinine changes and outcomes in patients admitted for acute heart failure: the cardio-renal syndrome revisited

Background: The changes in renal function that occurred in patients with acute decompensated heart failure (ADHF) are prevalent, and have multifactorial etiology and dissimilar prognosis. To what extent the prognostic role of such changes may vary according to the presence of renal insufficiency at admission is not clear. Accordingly, we sought to determine whether early creatinine changes (ΔCr) (admission to 48–72 hours) had an effect on 1-year mortality relative to the presence of renal insufficiency at admission. Methods: We included 705 consecutive patients admitted with the diagnosis of ADHF. Admission renal insufficiency was defined as serum creatinine ≥1.4mg/dl (A-RIcr) or estimated glomerular filtration rate <60ml/min/1.73m2 (A-RIGFR). Appropriate survival regression techniques were used. Results: The mean age was 72.9±11.4 years and 51.2% were males. Patients with admission renal insufficiency (24.7% and 42.8% for A-RIcr and A-RIGFR, respectively) had higher prevalence of extreme values in ΔCr in either direction (increasing/decreasing). At 1-year follow-up, 114 (16.2%) deaths were registered. The multivariable analysis showed a significant interaction between admission renal insufficiency and ΔCr (p=0.004 and p=0.019 for A-RIcr and A-RIGFR, respectively). In the presence of renal insufficiency, the continuum of ΔCr followed a positive and almost linear relationship with mortality risk. Conversely, in patients without renal insufficiency, those changes adopted a ‘J-shape’ trajectory with increased mortality at both ends of the curve distribution. Conclusions: In patients with ADHF the effect of ΔCr on 1-year mortality varied according to its magnitude and the presence of admission renal insufficiency. There was a graded-association with mortality when renal insufficiency was present on admission.
Distortion-Product Otoacoustic Emission Test Performance for Ototoxicity Monitoring

Introduction: A nonbehavioral method for monitoring ototoxicity in patients treated with cisplatin is needed because patients enduring chemotherapy may not be well or cooperative enough to undergo repeated hearing tests. Distortion-product otoacoustic emissions (DPOAEs) provide a nonbehavioral measure of auditory function that is sensitive to cisplatin exposure. However, interpreting DPOAE findings in the context of ototoxicity monitoring requires that their accuracy be determined in relation to a clinically accepted gold standard test. Objectives: Among patients receiving cisplatin for the treatment of cancer, we sought to (1) identify the combination of DPOAE metrics and ototoxicity risk factors that best classified ears with and without ototoxic-induced hearing changes; and (2) evaluate the test performance achieved by the composite measure as well as by DPOAEs alone. Design: Odds of experiencing hearing changes at a given patient visit were determined using data collected prospectively from 24 Veterans receiving cisplatin. Pure-tone thresholds were examined within an octave of each subject's high-frequency hearing limit. DPOAE were collected as a set of four response growth (input/output) functions near the highest f2 frequency that yielded a robust response at L2 = L1 = 65 dB SPL. Logistic regression modeled the risk of hearing change using several DPOAE metrics, drug treatment factors, and other patient factors as independent variables. An optimal discriminant function was derived by reducing the model so that only statistically significant variables were included. Receiver operating characteristic curve analyses were used to evaluate test performance. Results: At higher cisplatin doses, ears with better hearing at baseline were more likely to exhibit ototoxic hearing changes than those with poorer hearing. Measures of pre-exposure hearing, cumulative drug dose, and DPOAEs generated a highly accurate discriminant function with a cross-validated area under the receiver operating characteristic curve of 0.9. DPOAEs alone also provided an indication of ototoxic hearing change when measured at the highest DPOAE test frequency that yielded a robust response. Conclusions: DPOAEs alone and especially in combination with pre-exposure hearing and cisplatin dose provide an indication of whether or not hearing has changed as a result of cisplatin administration. These promising results need to be validated in a separate sample.
RI-MAC: a receiver-initiated asynchronous duty cycle MAC protocol for dynamic traffic loads in wireless sensor networks

The problem of idle listening is one of the most significant sources of energy consumption in wireless sensor nodes, and many techniques have been proposed based on duty cycling to reduce this cost. In this paper, we present a new asynchronous duty cycle MAC protocol, called Receiver-Initiated MAC (RI-MAC), that uses receiver-initiated data transmission in order to efficiently and effectively operate over a wide range of traffic loads. RI-MAC attempts to minimize the time a sender and its intended receiver occupy the wireless medium to find a rendezvous time for exchanging data, while still decoupling the sender and receiver's duty cycle schedules. We show the performance of RI-MAC through detailed ns-2 simulation and through measurements of an implementation in TinyOS in a testbed of MICAz motes. Compared to the prior asynchronous duty cycling approach of X-MAC, RI-MAC achieves higher throughput, packet delivery ratio, and power efficiency under a wide range of traffic loads. Especially when there are contending flows, such as bursty traffic or transmissions from hidden nodes, RI-MAC significantly improves throughput and packet delivery ratio. Even under light traffic load for which X-MAC is optimized, RI-MAC achieves the same high performance in terms of packet delivery ratio and latency while maintaining comparable power efficiency.
Serine Biosynthesis with One Carbon Catabolism and the Glycine Cleavage System Represents a Novel Pathway for ATP Generation

Previous experimental evidence indicates that some cancer cells have an alternative glycolysis pathway with net zero ATP production, implying that upregulation of glycolysis in these cells may not be related to the generation of ATP. Here we use a genome-scale model of human cell metabolism to investigate the potential metabolic alterations in cells using net zero ATP glycolysis. We uncover a novel pathway for ATP generation that involves reactions from serine biosynthesis, one-carbon metabolism and the glycine cleavage system, and show that the pathway is transcriptionally upregulated in an inducible murine model of Myc-driven liver tumorigenesis. This pathway has a predicted two-fold higher flux rate in cells using net zero ATP glycolysis than those using standard glycolysis and generates twice as much ATP with significantly lower rate of lactate - but higher rate of alanine secretion. Thus, in cells using the standard - or the net zero ATP glycolysis pathways a significant portion of the glycolysis flux is always associated with ATP generation, and the ratio between the flux rates of the two pathways determines the rate of ATP generation and lactate and alanine secretion during glycolysis.
Peginterferon Alfa-2a Is Associated with Elevations in Alanine Aminotransferase at the End of Treatment in Chronic Hepatitis C Patients with Sustained Virologic Response

Background The purpose of this study was to investigate the incidence and demographic/clinical factors of alanine aminotransferase (ALT) abnormalities at the end of treatment (EOT) in chronic hepatitis C (CHC) patients with sustained virologic response (SVR). Methods and Findings Seven hundred naïve CHC patients who underwent combination treatment between January 2003 and December 2010 were included in the study. The patients with SVR and serum ALT>upper limit of normal (ULN) at the EOT were further analyzed. The effects of clinical characteristics, treatment regimen, and virologic variables were evaluated by logistic regression. Of the 700 included patients, 488 (69.7%) achieved an SVR after treatment, and 235 (33.6%) had serum ALT levels>ULN at the EOT. Of those 488 patients, 137 (28.1%) had abnormal ALT values at the EOT. A multivariate analysis showed that the occurrence of ALT abnormalities at the EOT was significantly associated with pegylated interferon (PEG-IFN) alfa-2a (odds ratio [OR], 2.24; 95% confidence interval [CI], 1.45–3.45; P<0.001), baseline fatty liver (OR, 1.76; 95% CI, 1.16–2.76; P = 0.007), and baseline liver cirrhosis (OR, 2.35; 95% CI, 1.35–4.09; P = 0.002). Conclusions Use of PEG-IFN-alfa-2a, fatty liver, and cirrhosis are important factors associated with EOT-ALT abnormality in CHC patients receiving combination therapy that achieve an SVR. PEG-IFN-alfa-2a-related EOT-ALT elevation will become normal at the end of follow-up, but fatty liver and cirrhosis-related ALT elevation will not be resolved.
Assessment of pain in rheumatoid arthritis: minimal clinically significant difference, predictors, and the effect of anti-tumor necrosis factor therapy.

OBJECTIVE To compare a visual analog pain scale (VAS) with the Medical Outcomes Study Short Form-36 Health Survey (SF-36) bodily pain; to define the minimal clinically important change (MCIC) for pain in observational studies; to define clinically useful cutpoints for pain; to quantify the predictors of pain; and to estimate the effect of anti-tumor necrosis factor (TNF) therapy on pain. METHODS Over 6 years we studied 12,090 patients with rheumatoid arthritis (RA). Pain was assessed by VAS and SF-36 pain scales. RESULTS Compared with the SF-36 scale, the 0-10 VAS pain scale was better correlated with all clinical variables. The mean VAS score was 3.4 (standard deviation 2.8), and the best cutpoint for an "acceptable" level of pain was <or=2.0. The MCIC for pain was approximately 0.5 units by one measure and 1.1 by another. Pain increased slightly with the duration of RA, 0.03 (95% confidence interval 0.02-0.03) and decreased with age, 0.01 (95% CI 0.01-1.02) units per year. Pain was greater in ethnic minorities [0.78 (95% CI 0.63-0.93)] and women [0.31 (95% CI 0.23-0.39)] and was lower in college graduates [-0.88 (95% CI -1.00 to -0.76)]. Self-reported joint and nonarticular pain at 16 bilateral sites explained 44% of VAS pain scores. Anti-TNF therapy reduced pain by 0.59 to 0.53 units and EuroQol utility by 0.02 (95% CI 0.02-0.02) units. CONCLUSION Anti-TNF therapy improved pain by 0.53 to 0.70 units. The MCIC for improvement and worsening of pain is about 0.5 to 1.1 units. Pain levels are almost constant over RA duration, and are increased in women, ethnic minorities, smokers, and those with less education.
Trauma research in the Baltic countries: from political oppression to recovery

The aim of this paper is to provide an overview of traumatic stress studies from the three Baltic countries—Lithuania, Latvia, and Estonia—and reveal how specific social context contributes to the topics relevant in traumatic stress field in the region. Traumatic stress studies in the Baltic countries are closely related to the complicated history of the region. It was only since the restoration of independence of the Baltic States in the 1990s when traumatic stress studies could emerge. The start of the psychotraumatology in the Baltic States was inspired by the interest of the psychological effects of political violence. Four major topics in traumatic stress literature from the Baltic countries were identified in this article: political violence studies, epidemiology of trauma and posttraumatic stress disorder (PTSD), disaster studies, and developmental aspects of trauma. Traumatic events prevalence was reported between 70 and 75%, and PTSD prevalence range 2–7% in the Baltic countries. The interest in psychotraumatology in the Baltic countries is rising.
The Use of Phytase and Low Phosphorus Levels in Broiler Diets with Different Metabolizable Energy Levels

The objective of this study was to determine the effects of dietary available phosphorus (AP), phytase supplementation and metabolizable energy (ME) levels on performance and bone and blood characteristics of broiler chickens. An experiment in completely randomized design with 2 × 2 × 2 factorial arrangement were conducted, in which two phytase levels (0 and 500 mg/kg), two AP levels (NRC and 15% lower) and two ME levels were used. The ME ratios to CP and other nutrients (except phosphorus) were equal in all treatments. Average weight gain, feed intake, and feed conversion ratio (FCR) of starter, grower and total rearing period were analyzed. Bone calcium and phosphorus, blood calcium, phosphorus and alkaline phosphatase at 6 weeks of age were analyzed. Based on growth parameters, low AP level had equal or better effects than high AP level. Chickens fed diets with high ME levels had better performance. Phytase had no significant effects on weight gain, whereas it enhanced FCR. Adding phytase in low energy diets improved body weight gain and FCR. Phytase in diets with low AP levels significantly enhanced FCR. Using low AP in high and low energy diets, caused better FCR in starter and whole rearing phase consequently. Available phosphorus and phytase supplementations had no significant effects on tibia ash; however, it was inversely affected by low AP level. The results of this experiment indicated that it is possible to decrease dietary AP level up to 15 percent less than NRC recommends. Adding AP and phytase did not significantly affect growth parameters of the chicks fed low energy diets.
Alteration of some functional and metabolic characteristics of resident mouse peritoneal macrophages by lymphocyte mediators

Resident mouse peritoneal macrophages were incubated in Sephadex G-100 fractions of supernates from concanavalin A-stimulated lymphocytes. A significant effect of the lymphocyte supernatant fractions containing mediators on macrophage 5'-nucleotidase, glucose-1 14C oxidation, cell maintenance, and migration is reported. The 5'-nucleotidase was depressed to an extent similar to that seen in activated macrophages obtained from Listeria-infected mice. On the other hand, glucose-1-14C oxidation was enhanced, but not to the same degree as seen in the counterparts in vivo. Whereas migration inhibitory factor (MIF) and cell adherence-augmenting activity were found in a number of adjacent fractions, the metabolic effects were found predominantly in a single fraction. Resident peritoneal macrophages or those elicited by the injection of a lymphocyte-derived chemotactic factor were more responsive with respect to the biochemical changes than caseinate- elicited macrophages. On the other hand, caseinate-elicited macrophages appeared to be more sensitive with respect to the effects of mediator(s) on cell retention. A possible dissociation between MIF and cell-adherence augmenting activity, on the one hand, and the entities that stimulate glucose-1-14C oxidation is reported, based on fractionation studies, and loss of the latter activity upon storage of lymphocyte supernates.
Deep Temporal Appearance-Geometry Network for Facial Expression Recognition

Temporal information can provide useful features for recognizing facial expressions. However, to manually design useful features requires a lot of effort. In this paper, to reduce this effort, a deep learning technique which is regarded as a tool to automatically extract useful features from raw data, is adopted. Our deep network is based on two different models. The first deep network extracts temporal geometry features from temporal facial landmark points, while the other deep network extracts temporal appearance features from image sequences . These two models are combined in order to boost the performance of the facial expression recognition. Through several experiments, we showed that the two models cooperate with each other. As a result, we achieved superior performance to other state-of-the-art methods in CK+ and Oulu-CASIA databases. Furthermore, one of the main contributions of this paper is that our deep network catches the facial action points automatically.
Structured Multiple Endosymbiosis of Bacteria and Archaea in a Ciliate from Marine Sulfidic Sediments: A Survival Mechanism in Low Oxygen, Sulfidic Sediments?

Marine micro-oxic to sulfidic environments are sites of intensive biogeochemical cycling and elemental sequestration, where prokaryotes are major driving forces mediating carbon, nitrogen, sulfur, phosphorus, and metal cycles, important from both biogeochemical and evolutionary perspectives. Associations between single-celled eukaryotes and bacteria and/or archaea are common in such habitats. Here we describe a ciliate common in the micro-oxic to anoxic, typically sulfidic, sediments of Santa Barbara Basin (CA, USA). The ciliate is 95% similar to Parduzcia orbis (18S rRNA). Transmission electron micrographs reveal clusters of at least three different endobiont types organized within membrane-bound sub-cellular regions. Catalyzed reporter deposition–fluorescent in situ hybridization and 16S rRNA clone libraries confirm the symbionts include up to two sulfate reducers (Desulfobulbaceae, Desulfobacteraceae), a methanogen (Methanobacteriales), and possibly a Bacteroidete (Cytophaga) and a Type I methanotroph, suggesting synergistic metabolisms in this environment. This case study is discussed in terms of implications to biogeochemistry, and benthic ecology.
Autonomous Bidding Agents in the Trading Agent Competition

Designing agents that can bid in online simultaneous auctions is a complex task. The authors describe task-specific details and strategies of agents in a trading agent competition. More specifically, the article describes the task-specific details of and the general motivations behind, the four top-scoring agents. First, we discuss general strategies used by most of the participating agents. We then report on the strategies of the four top-placing agents. We conclude with suggestions for improving the design of future trading agent competitions.
Model-independent search for CP violation in D 0 → K − K + π − π + and D 0 →

A search for CP violation in the phase-space structures of D0 and D0 decays to the final states K−K+π−π+ and π−π+π+π− is presented. The search is carried out with a data set corresponding to an integrated luminosity of 1.0 fb−1 collected in 2011 by the LHCb experiment in pp collisions at a centre-of-mass energy of 7 TeV. For the K−K+π−π+ final state, the four-body phase space is divided into 32 bins, each bin with approximately 1800 decays. The p-value under the hypothesis of no CP violation is 9.1%, and in no bin is a CP asymmetry greater than 6.5% observed. The phase space of the π−π+π+π− final state is partitioned into 128 bins, each bin with approximately 2500 decays. The p-value under the hypothesis of no CP violation is 41%, and in no bin is a CP asymmetry greater than 5.5% observed. All results are consistent with the hypothesis of no CP violation at the current sensitivity. Submitted to Phys. Lett. B c © CERN on behalf of the LHCb collaboration, license CC-BY-3.0. †Authors are listed on the following pages. ar X iv :1 30 8. 31 89 v2 [ he pex ] 2 S ep 2 01 3
Disabling Vertigo and Tinnitus Caused by Intrameatal Compression of the Anterior Inferior Cerebellar Artery on the Vestibulocochlear Nerve: A Case Report, Surgical Considerations, and Review of the Literature

Abstract Microvascular compression of the vestibulocochlear nerve is known as a cause of tinnitus and vertigo in the literature, but our review of the literature shows that the compression is usually located in the cerebellopontine angle and not intrameatal. We present a case of intrameatal compression of the anterior inferior cerebellar artery (AICA) on the vestibulocochlear nerve of a 40-year-old woman with symptoms of disabling vertigo and intermittent high-frequency tinnitus on the left side without any hearing loss for ∼ 4 years. Magnetic resonance imaging of the brain did not show any abnormality, but magnetic resonance angiography showed a left intrameatal AICA loop as a possible cause of the disabling symptoms. After the exclusion of other possible reasons for disabling vertigo, surgery was indicated. The intraoperative findings proved the radiologic findings. The large AICA loop was found extending into the internal auditory canal and compressing the vestibulocochlear nerve. The AICA loop was mobilized and separated from the vestibulocochlear nerve. The patient's symptoms resolved immediately after surgery, and no symptoms were noted during 2 years of follow-up in our clinic. Her hearing was not affected by the surgery. In addition to other common reasons, such as acoustic neuroma, disabling vertigo and tinnitus can occur from an intrameatal arterial loop compression of the vestibulocochlear nerve and may be treated successfully by drilling the internal acoustic meatus and separating the arterial conflict from the vestibulocochlear nerve.