Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis of Triacylglycerols by the Acyl-Coenzyme A:Diacyl-Glycerol Acyltransferase Dga1p in Lipid Particles of the Yeast Saccharomyces cerevisiae

ABSTRACT The terminal step of triacylglycerol (TAG) formation in the yeast Saccharomyces cerevisiae is catalyzed by the enzyme acyl-CoA:diacylglycerol acyltransferase (DAGAT). In this study we demonstrate that the gene product of YOR245c, Dga1p, catalyzes a major yeast DAGAT activity which is localized to lipid particles. Enzyme measurements employing a newly established assay containing radioactively labeled diacylglycerol (DAG) as a substrate and unlabeled palmitoyl-CoA as a cosubstrate revealed a 70- to 90-fold enrichment of DAGAT in lipid particles over the homogenate but also a 2- to 3-fold enrichment in endoplasmic reticulum fractions. In a dga1 deletion strain, the DAGAT activity in lipid particles is dramatically reduced, whereas the activity in microsomes is affected only to a minor extent. Thus, we propose the existence of DAGAT isoenzymes in the microsomal fraction. Furthermore, we unveiled an acyl-CoA-independent TAG synthase activity in lipid particles which is distinct from Dga1p and the phosphatidylcholine:DAGAT Lro1p. This acyl-CoA-independent TAG synthase utilizes DAG as an acceptor and free fatty acids as cosubstrates and occurs independently of the acyl-CoA synthases Faa1p to Faa4p. Based on lipid analysis of the respective deletion strains, Lro1p and Dga1p are the major contributors to total cellular TAG synthesis, whereas other TAG synthesizing systems appear to be of minor importance. In conclusion, at least three different pathways are involved in the formation of storage TAG in the yeast.
Neuroscience for the Mental Health Clinician

Introduction. Part 1: Basic Principles of Neuroscience. Draw the Brain: Introduction to Clinical Neuroanatomy. The Neuron. Neurotransmitters. Fear, Reward, and Action. Memory. An Overview of Cortical Function. Part 2: Neuroscience of Mental Disorders. Introduction to Clinical Issues. Attention-Deficit/Hyperactivity Disorder. Aggression, Antisocial Behavior, and Substance Abuse. Mood and Anxiety Disorders. Schizophrenia and Pervasive Developmental Disorders. Cognitive Disorders. Epilogue.
A probabilistic measure for alignment-free sequence comparison

MOTIVATION Alignment-free sequence comparison methods are still in the early stages of development compared to those of alignment-based sequence analysis. In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models. RESULTS The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free). AVAILABILITY All datasets and computer codes written in MATLAB are available upon request from the first author.
Mutation at chromosome 11q23 in human non‐familial breast cancer: A microdissection microsatellite analysis

Allelotypic evaluation of loss of heterozygosity (LOH) has been instrumental in the identification of tumour suppressor genes. Here we report a high incidence of LOH at chromosome 11q23 in non‐familial breast cancers with in situ, invasive, and metastatic tumour cells microdissected from archival haematoxylin and eosin (H & E) sections for polymerase chain reaction (PCR)‐LOH analysis at polymorphic microsatellite loci. Ninety‐four cases of non‐familial breast cancer were examined at the D11S29 microsatellite locus on chromosome 11q23. Eighty‐three cases (88 per cent) were informative and 35 cases overall (42 per cent) had LOH at this locus, comprising 23 per cent of in situ, 36 per cent of invasive, and 28 per cent of metastatic cancers. The DNA from those cancer cells with LOH was amplified at microsatellite loci D11S554 (11p12–p11.2) and D11S534 (11q13). In 19 of 67 cases overall (28 per cent), LOH occurred solely at 11q23. There was an association between LOH at 11q23 and tumour size ≥2 cm (P<0.01) in the overall results and the invasive cancers. The data revealed heterogeneity for LOH at D11S29 in in situ, invasive, and metastatic cells from the same case. In general, however, there was concordance between LOH (or its absence) in in situ and invasive disease. We conclude that the distal part of the long arm of chromosome 11 contains a region involved in breast carcinogenesis and that there is molecular heterogeneity at this chromosomal region in individual breast cancer cells.
Comparative Studies of Salivary and Blood Sialic Acid, Lipid Peroxidation and Antioxidative Status in Oral Squamous Cell Carcinoma (OSCC)

Objective : Oral squamous cell carcinoma (OSCC) is considered to be a serious life threatening issue for almost two decades. The objective of this study was to evaluate the over production of lipid peroxidation (LPO) byproducts and disturbances in antioxidant defense system in the pathogenesis of oral cancer. Methods : Lipid peroxidation and antioxidant status in OSCC patients were estimated and compared the sensitivity and specificity of circulating biomarkers (MDA, Sialic acid, Catalase, SOD, GSH and Neuraminidase) with β-2 microglobulin (β-2MG) at different thresholds in blood and saliva using receiver operating characteristics (ROC) curve design. R esults : Our results showed that the levels of MDA and Sialic acid were significantly increased in plasma of OSCC patients as compared to healthy subjects whereas antioxidant level was significantly decreased. Conclusion : ROC analysis indicated that MDA in saliva is a better diagnostic tool as compared to MDA in blood and β-2MG in blood is better diagnostic marker as compared to β-2MG level in saliva.
Nonlinear Filters Based Fault Diagnosis in Nonlinear Stochastic Systems

Three methods for fault diagnosis in nonlinear stochastic systems are studied in this paper, which are based on extended Kalman filter (EKF), unscented Kalman filter (UKF), and particle filter (PF). Multiple-model based fault detector and fault classification method with the likelihood ratio test are applied to fault diagnosis of nonlinear systems. In various noise environments, the comparative studies have been carried out on the fault detection and diagnosis for nonlinear stochastic systems with EKF, UKF and PF, respectively. Simulations demonstrate the effectiveness of the fault diagnosis method based on the PF in nonlinear and non-Gauassian stochastic systems.
Carbon storage in young growth coast redwood stands

Carbon sequestration is an emerging forest management objective within California and around the world. With the passage of the California's Global Warming Solutions Act (AB32) our need to understand the dynamics of carbon sequestration and to accurately measure carbon storage is essential to insure successful implementation of carbon credit projects throughout the State. As the leader in forest carbon credit projects within the U.S., California's forest carbon protocols are being looked to as templates for successful carbon credit accounting. Coast redwood (Sequoia sempervirens) stands have the largest measured biomass per acre making the argument for use of the species in long-term carbon sequestration projects self evident. To date no direct measurement of both carbon fraction and wood density of coast redwood has been undertaken. With this study we tested the applicability of the current forest carbon project protocols set out by the Climate Action Reserve for forest carbon credit projects within California. Specifically we tested the applicability of a carbon fraction of 0.5 and a greenwood density of 0.34 g/cm3 for coast redwood trees. Our main findings were that: 1) a species-average of 0.34 g/cm3 significantly underestimated the wood density of the measured trees, 2) wood density varied predictably with tree height and wood type, 3) carbon fraction was significantly higher than the default 0.5, and 4) carbon fraction varied predictably in relation to wood type. Our results indicate that a simple approach to estimating carbon storage utilizing a carbon fraction of 0.5 and a species-average wood density underestimates carbon budgets in young growth redwood stands. Given the regional nature of carbon credit projects our results indicate that forest project protocols should be adjusted to allow for calculations that incorporate directly measured wood density and carbon fraction values within the forest carbon project area.
Structural and Functional Insight into How the Plasmodium falciparum VAR2CSA Protein Mediates Binding to Chondroitin Sulfate A in Placental Malaria*

Background: VAR2CSA expressing Plasmodium falciparum parasites cause placental malaria by interacting with chondroitin sulfate A (CSA) on placental syncytiotrophoblasts. Results: The CSA-binding site in VAR2CSA lies within the N-terminal DBL2X domain, which maps to the center of the compact VAR2CSA structure. Conclusion: VAR2CSA fragments based on the CSA-binding region are potent vaccine candidates. Significance: The data presented has important implications for vaccine development. Malaria is a major global health problem. Pregnant women are susceptible to infection regardless of previously acquired immunity. Placental malaria is caused by parasites capable of sequestering in the placenta. This is mediated by VAR2CSA, a parasite antigen that interacts with chondroitin sulfate A (CSA). One vaccine strategy is to block this interaction with VAR2CSA-specific antibodies. It is a priority to define a small VAR2CSA fragment that can be used in an adhesion blocking vaccine. In this, the obvious approach is to define regions of VAR2CSA involved in receptor binding. It has been shown that full-length recombinant VAR2CSA binds specifically to CSA with nanomolar affinity, and that the CSA-binding site lies in the N-terminal part of the protein. In this study we define the minimal binding region by truncating VAR2CSA and analyzing CSA binding using biosensor technology. We show that the core CSA-binding site lies within the DBL2X domain and parts of the flanking interdomain regions. This is in contrast to the idea that single domains do not possess the structural requirements for specific CSA binding. Small-angle x-ray scattering measurements enabled modeling of VAR2CSA and showed that the CSA-binding DBL2X domain is situated in the center of the structure. Mutating classic sulfate-binding sites in VAR2CSA, along with testing dependence of ionic interactions, suggest that the CSA binding is not solely dependent on the sulfated CSA structure. Based on these novel PfEMP1 structure-function studies, we have constructed a small VAR2CSA antigen that has the capacity to induce highly adhesion-blocking antibodies.
Diet quality and weight gain among black and white young adults: the Coronary Artery Risk Development in Young Adults (CARDIA) Study (1985-2005).

BACKGROUND Little is known about the long-term health consequences of following the 2005 Dietary Guidelines for Americans (DGA; Washington, DC: US Government Printing Office, 2005). OBJECTIVE The objective was to examine the longitudinal association between diets consistent with the 2005 DGA and subsequent weight gain. DESIGN We used data from the Coronary Artery Risk Development in Young Adults (CARDIA) Study, a cohort of black and white men and women aged 18-30 y at baseline who attended ≤7 examinations from 1985-1986 to 2005-2006 (n = 4913). We created a 100-point Diet Quality Index (2005 DQI) to rate participants' diets based on meeting the 2005 DGA key recommendations. Longitudinal models of weight gain were adjusted for physical activity, smoking, energy intake, age, education, sex, and initial body mass index (BMI) and included interaction terms of DQI by race and initial BMI (if statistically significant). RESULTS We found effect modification by race (likelihood ratio test, P < 0.03 in all models). The mean adjusted 20-y weight change was +19.4 kg for blacks and +11.2 kg for whites with high diet quality (DQI >70) and +17.8 for blacks and +13.9 for whites with a DQI <50 (P < 0.05). In race-specific Cox models (with interaction terms for DQI × initial BMI, P < 0.05), a 10-point increase in DQI score was associated with a 10% lower risk of gaining 10 kg in whites with an initial BMI (in kg/m(2)) <25 but with a 15% higher risk in blacks with baseline obesity (P < 0.001). CONCLUSIONS Our findings do not support the hypothesis that a diet consistent with the 2005 DGA benefits long-term weight maintenance in American young adults. Greater need for attention to obesity prevention in future DGAs is warranted.
The Treatment of Neuroleptic Malignant Syndrome are Dantrolene and Bromocriptine Useful Adjuncts to Supportive Care?

In a prospective study of 20 patients with NMS, those who received dantrolene (2 patients) or bromocriptine (2 patients) or both (4 patients) tended to have a more prolonged course of illness and a greater incidence of sequelae than those treated with supportive care alone. These results do not indicate a useful role for dantrolene or bromocriptine in the treatment of NMS.
Journal of Graph Algorithms and Applications Drawing 3-polytopes with Good Vertex Resolution 34 André Schulz Drawing 3-polytopes with Good Vertex Resolution

We study the problem how to obtain a small drawing of a 3-polytope with Euclidean distance between any two points at least 1. The problem can be reduced to a one-dimensional problem, since it is sufficient to guarantee distinct integer x-coordinates. We develop an algorithm that yields an embedding with the desired property such that the polytope is contained inside a 2(n − 2) × 2 × 1 box. The constructed embedding can be scaled to a grid embedding whose x-coordinates are contained in [0, 2(n − 2)]. Furthermore, the point set of the embedding has a small spread, which differs from the best possible spread only by a multiplicative constant.
SSEP in Therapeutic Hypothermia Era

Purpose: The reliability of somatosensory evoked potentials (SSEPs) in predicting outcome in comatose survivors of cardiac arrest treated with therapeutic hypothermia (TH) has been questioned. We investigated whether the absence of cortical (N20) responses was a reliable predictor of a nonawakening in the setting of TH. Methods: A retrospective review was conducted in cardiac arrest survivors treated with TH admitted to a single tertiary care hospital from April, 2010 to March, 2013 who underwent SSEP testing at various time points after cardiac arrest. N20 responses were categorized as normal, present but abnormal, bilaterally absent, or inadequate for interpretation. Neurologic outcome was assessed at discharge by the Cerebral Performance Category Scale (CPC). Results: Ninety-three SSEP studies were performed in 73 patients. Fourteen patients had absent N20 responses; all had poor outcome (CPC 4–5). Eleven patients had absent N20 s during hypothermia, three of whom had follow-up SSEPs after rewarming and cortical responses remained absent. Fifty-seven patients had N20 peaks identified and had variable outcomes. Evaluation of 1 or more N20 peaks was limited or inadequate in 11.4% of SSEPs performed during the cooling because of artifact. Conclusions: Somatosensory evoked potentials remain a reliable prognostic indicator in patients undergoing TH. The limited sample size of patients who had SSEP performed during TH and repeated after normothermia added to the effect of self-fulfilling prophecy limit the interpretation of the reliability of this testing when performed during cooling. Further prospective, multicenter, large scale studies correlating cortical responses in SSEPs during and after TH are warranted. Technical challenges are commonplace during TH and caution is advised in the interpretation of suboptimal recordings.
Modulation of stress reactivity in brain and body by serotonin transporter promoter polymorphism1

The polymorphism of the serotonin transporter gene in the promoter region (5HTTLPR) has been considered to link with vulnerability to depression and anxiety. This paper introduces a series of our studies showing that this genetic polymorphism can explain portions of individual differences in stress reactivity at multiple levels: brain functions, peripheral physiological responses, and behaviors. Specifically: (a) carriers of double short (S) alleles, compared with carriers of at least one long (L) allele, show greater activation in the hypothalamus and larger reactivity in blood catecholamine, cortisol, and an inflammatory cytokine to acute stress; (b) carriers of double S alleles are more sensitive to punishment, and thus show poorer performance in a decision-making situation where they have to stick to a long-term correct option regardless of short-term punishment; and (c) carriers of double S alleles show greater activation of the amygdala and a correlation between amygdalar activity and an increase of natural killer cell proportion in blood when positive emotions are elicited. A possible model to explain the biological mechanisms underlying those phenomena is proposed and the ecological adaptive values of the 5HTTLPR genotypes are discussed.
EM-Based Optimal Maximal Ratio Diversity Combiner for Constant Envelope Signals

An optimal maximal ratio combiner (MRC) based on the expectation-maximization (EM) algorithm is devel- oped for noisy constant envelope signals transmitted over a Rayleigh fading channel. Instead of using a transmitted pilot signal with the data to estimate the combiner gains, the EM algorithm is used to perform this estimation. In the developed MRC, estimation of the transmitted data sequence is performed also by the EM algorithm. Estimation using the EM algo- rithm provides an iterative solution to the maximum likelihood (ML) approach. Therefore, the resulting receiver is opti- mum and does not suffer from the difficulties resulted from direct application of the ML procedure. One of these difficul- ties is the computational complexity which depends exponentially on the data sequence length. Introducing an iterative structure in the developed MRC achieves a linear computational complexity and enables efficient data extraction by the Viterbi algorithm when trellis coding is used.
Hardening Stratum, the Bitcoin Pool Mining Protocol

Abstract Stratum, the de-facto mining communication protocol used by blockchain based cryptocurrency systems, enables miners to reliably and efficiently fetch jobs from mining pool servers. In this paper we exploit Stratum’s lack of encryption to develop passive and active attacks on Bitcoin’s mining protocol, with important implications on the privacy, security and even safety of mining equipment owners. We introduce StraTap and ISP Log attacks, that infer miner earnings if given access to miner communications, or even their logs. We develop BiteCoin, an active attack that hijacks shares submitted by miners, and their associated payouts. We build BiteCoin on WireGhost, a tool we developed to hijack and surreptitiously maintain Stratum connections. Our attacks reveal that securing Stratum through pervasive encryption is not only undesirable (due to large overheads), but also ineffective: an adversary can predict miner earnings even when given access to only packet timestamps. Instead, we devise Bedrock, a minimalistic Stratum extension that protects the privacy and security of mining participants. We introduce and leverage the mining cookie concept, a secret that each miner shares with the pool and includes in its puzzle computations, and that prevents attackers from reconstructing or hijacking the puzzles. We have implemented our attacks and collected 138MB of Stratum protocol traffic from mining equipment in the US and Venezuela. We show that Bedrock is resilient to active attacks even when an adversary breaks the crypto constructs it uses. Bedrock imposes a daily overhead of 12.03s on a single pool server that handles mining traffic from 16,000 miners.
Current Management of Vascular Infections

Technical advances in Vascular Surgery have led to an increased use of prostheses (grafts, patches, stents, stent grafts etc.) and improved results for the patient. Despite routine antibiotic prophylaxis, infection, although rare, remains a serious complication, with catastrophic consequences. Vascular infections are divided into 3 groups according to Szilagyi (Table 1.), depending on the extent of the inflammation: the superficial, the deep and the mixed type. [1] Samson (Table 1.), as well as Karl and Storck (Table 1.) , have modified the widely used classification system of Szilagyi. [1-3] While the superficial type is restricted to the skin and subcutaneous tissue, the deep infection involves the vessels or a prosthetic graft. The mixed type of vascular infection is the combination of the above types affects all the tissue layers and can produce trauma disruption. Vascular infections can be classified by appearance time into: a) early ( 4 weeks). Samson’s and Karl’s modifications take into consideration further clinical parameters, which define the treatment (Table 2.). [2,3] When infection involves a graft anastomosis or the suture line of a patch, there is high risk of vessel rupture, septic hemorrhage or pseudoaneurysm formation. [4-6] Other serious complications are septic thrombosis, endocarditis, etc. [7] In severe cases, treatment can be problematic and mortality remains high, despite the use of antibiotics and surgical treatment. Keys to successful outcome include early and accurate diagnosis, identification of the infecting organism, and extent of graft infection, administration of culture-specific antibiotic therapy, and excision or replacement of the infected graft.
Changes over time in socioeconomic inequalities in breast and rectal cancer survival in England and Wales during a 32-year period (1973-2004): the potential role of health care.

BACKGROUND Socioeconomic inequalities in cancer survival are well documented but they vary for different cancers and over time. Reasons for these differences are poorly understood. PATIENTS AND METHODS For England and Wales, we examined trends in socioeconomic survival inequalities for breast cancer in women and rectal cancer in men during the 32-year period 1973-2004. We used a theoretical framework based on Victora's 'inverse equity' law, under which survival inequalities could change with the advent of successive new treatments, of varying effectiveness, which are disseminated with different speed among patients of different socioeconomic groups. We estimated 5-year relative survival for patients of different deprivation quintiles and examined trends in survival inequalities in light of major treatment innovations. RESULTS Inequalities in breast cancer survival (921,611 cases) narrowed steadily during the study (from -10% to -6%). In contrast, inequalities in rectal cancer survival (187,104 cases) widened overall (form -5% to -11%) with fluctuating periods of narrowing inequality. CONCLUSIONS Trends in socioeconomic differences in tumour or patient factors are unlikely explanations of observed changes over time in survival inequalities. The sequential introduction into clinical practice of new treatments of progressively smaller incremental benefit may partly explain the reduction in inequality in breast cancer survival.