Miracle-dz/UniFAR-FTUs huggingface dataset:
The alcoholic phenotypes among different multidimensional typologies: similarities and their classification procedures.

AIM This detailed cross-sectional analysis, obtained from a sample of alcohol-dependent patients, attempts to compare multiple methods that have been created to classify or subtype alcoholics. METHODS The sample comprised 318 alcohol-dependent patients recruited from the alcoholism unit (NETER) of the Psychiatric Service of Santa Maria University Hospital in Lisbon (Portugal). All subjects were evaluated during the outpatient therapeutical programme for operationalized criteria, reported by each alcoholism typology. RESULTS Regarding concordance agreement (kappa values) for the three type I/II classifications, von Knorring versus Sullivan yielded the higher rate of agreement, followed by von Knorring versus Gilligan and Gilligan versus Sullivan criteria. Chi-square comparisons showed a significant overlap between Babor type A and Cloninger type I of von Knorring and Sullivan. Over-two-type classifications showed the following significant positive relations: Lesch type I versus NETER heredopathic subtype; Lesch type II versus NETER anxiopathic subtype and Babor type A; Lesch type III versus NETER tymopathic subtype; Lesch type IV versus Cloninger type II of von Knorring and Sullivan criteria; and NETER adictopathic subtype versus Cloninger type II of von Knorring, Sullivan and Gilligan criteria. CONCLUSIONS There is a significant overlap across many of the multivariate alcoholic subtypes purposed, in which much of the concordance is a function of common characteristics in subtype operationalization. Commonalities among these different subtyping classification systems offers the possibility of identifying important dimensions that better differentiate individuals among problem drinker's populations.
Infection with Chlamydia pneumoniae accelerates the development of atherosclerosis and treatment with azithromycin prevents it in a rabbit model.

BACKGROUND Chlamydia pneumoniae infection has been associated with atherosclerosis by serological studies and detection of bacterial antigen within plaque. We sought to evaluate a possible causal role in an animal model. METHODS AND RESULTS Thirty New Zealand White rabbits were given three separate intranasal inoculations of either C pneumoniae (n = 20) or saline (n = 10) at 3-week intervals and fed chow enriched with a small amount (0.25%) of cholesterol. Immediately after the final inoculation, infected and control rabbits were randomized and begun on a 7-week course of azithromycin or no therapy. Three months after the final inoculation, rabbits were euthanatized and sections of thoracic aortas were blindly evaluated microscopically for maximal intimal thickness (MIT), percentage of luminal circumference involved (PLCI), and plaque area index (PAI) of atherosclerosis. Vascular chlamydial antigen was assessed by direct immunofluorescence. MIT differed among treatment groups (P=.009), showing an increase in infected rabbits (0.55 mm; SE = 0.15 mm) compared with uninfected controls (0.16 mm; SE = 0.06 mm) and with infected rabbits receiving antibiotics (0.20 mm; SE = 0.03 mm) (both P<.025), whereas MIT in infected/treated versus control rabbits did not differ. PLCI also tended to differ (P<.1) and PAI differed significantly (P<.01) among groups with a similar pattern. Chlamydial antigen was detected in 2 untreated, 3 treated, and 0 control animals. CONCLUSIONS Intranasal C pneumoniae infection accelerates intimal thickening in rabbits given a modestly cholesterol-enhanced diet. In addition, weekly treatment with azithromycin after infectious exposure prevents accelerated intimal thickening. These findings strengthen the etiologic link between C pneumoniae and atherosclerosis and should stimulate additional animal and human studies, including clinical antibiotic trials.
Statistics of work and fluctuation theorems for microcanonical initial states

Work performed on a system in a microcanonical state by changes in a control parameter is characterized in terms of its statistics. The transition probabilities between eigenstates of the system Hamiltonians at the beginning and the end of the parameter change obey a detailed balance-like relation from which various forms of the microcanonical fluctuation theorem are obtained. As an example, sudden deformations of a two-dimensional harmonic oscillator potential are considered, and the validity of the microcanonical Jarzynski equality connecting the degrees of degeneracy of energy eigenvalues before and after the control parameter change is confirmed.
In Silico Evaluation of an Artificial Pancreas Combining Exogenous Ultrafast-Acting Technosphere Insulin with Zone Model Predictive Control

Background: Because of the slow pharmacokinetics of subcutaneous (SC) insulin, avoiding postprandial hyperglycemia has been a major challenge for an artificial pancreas (AP) using SC insulin without a meal announcement. Methods: A semiautomated AP with Technosphere® Insulin (TI; MannKind Corporation, Valencia, CA) was designed to combine pulmonary and SC insulin. Manual inhalation of 10 U ultrafast-absorbing TI at mealtime delivers the first, or cephalic, phase of insulin, and an SC insulin pump controlled by zone model predictive controller delivers second-phase and basal insulin. This AP design was evaluated on 100 in silico subjects from the University of Virginia/Padova metabolic simulator using a protocol of two 50 g carbohydrate (CHO) meals and two 15 g CHO snacks. Results: Simulation analysis shows that the semiautomated AP with TI provides 32% and 16% more time in the controller target zone (80–140 mg/dl) during the 4 h postprandial period, with 39 and 20 mg/dl lower postprandial blood glucose peak on average than the pure feedback AP and the AP with manual feed-forward SC bolus, respectively. No severe hypoglycemia (<50 mg/dl) was observed in any cases. Conclusions: The semiautomated AP with TI provides maximum time in the clinically accepted region when compared with pure feedback AP and AP with manual feed-forward SC bolus. Furthermore, the semiautomated AP with TI provides a flexible operation (optional TI inhalation) with minimal user interaction, where the controller design can be tailored to specific user needs and abilities to interact with the device.
A Mathematical Model for the Intracellular Circadian Rhythm Generator

A mathematical model for the intracellular circadian rhythm generator has been studied, based on a negative feedback of protein products on the transcription rate of their genes. The study is an attempt at examining minimal but biologically realistic requirements for a negative molecular feedback loop involving considerably faster reactions, to produce (slow) circadian oscillations. The model included mRNA and protein production and degradation, along with a negative feedback of the proteins upon mRNA production. The protein production process was described solely by its total duration and a nonlinear term, whereas also the feedback included nonlinear interactions among protein molecules. This system was found to produce robust oscillations in protein and mRNA levels over a wide range of parameter values. Oscillations were slow, with periods much longer than the time constants of any of the individual system parameters. Circadian oscillations were obtained for realistic values of the parameters. The system was readily entrainable to external periodic perturbations. Two distinct classes of phase response curves were found, viz. with or without a time domain within the circadian cycle in which external perturbations fail to induce a phase shift (“dead zone”). The delay and nonlinearity in the protein production and the cooperativity in the negative feedback (Hill coefficient) were for this model found to be necessary and sufficient to generate robust circadian oscillations. The similarities between model outcomes and empirical findings establish that circadian rhythmicity at the cellular level can plausibly emerge from interactions among molecular systems which are not in themselves rhythmic.
Neural networks with transient state dynamics

We investigate dynamical systems characterized by a time series of distinct semi-stable activity patterns, as they are observed in cortical neural activity patterns. We propose and discuss a general mechanism allowing for an adiabatic continuation between attractor networks and a specific adjoined transient-state network, which is strictly dissipative. Dynamical systems with transient states retain functionality when their working point is autoregulated—avoiding prolonged periods of stasis or drifting into a regime of rapid fluctuations. We show, within a continuous-time neural network model, that a single local updating rule for online learning allows simultaneously (i) for information storage via unsupervised Hebbian-type learning, (ii) for adaptive regulation of the working point and (iii) for the suppression of runaway synaptic growth. Simulation results are presented; the spontaneous breaking of time-reversal symmetry and link symmetry are discussed.
Long-term results after resection of bronchial carcinoid tumour: evaluation of survival and prognostic factors.

OBJECTIVES We retrospectively analysed morbidity, mortality and oncological results of patients who had undergone surgery for bronchial carcinoid tumours. METHODS Between 2002 and 2012, 65 patients with bronchial carcinoids underwent lobectomy (n = 34), sublobar resection (segmentectomy/wedge) (n = 18), sleeve lobectomy (n = 5) (reconstruction of the pulmonary artery was associated in 1 case), sleeve resection of the main bronchus (n = 4) or pneumonectomy (n = 4) (reconstruction of the carina was associated in 1 case). RESULTS Resection was radical with histologically negative margins in all patients (R0). Histology showed typical carcinoid (TC) in 55 (84.6%) patients and atypical carcinoid (AC) in 10 (15.4%) patients. Final pathological stages were Stage I in 42 (64.6%) patients, Stage II in 18 (27.7%) and Stage III in 5 (7.7%). No postoperative mortality was observed. The postoperative morbidity rate was 15.4% (no bronchial and/or vascular reconstructive-related complications occurred). The median follow-up was 58 (range 2-121) months. The overall recurrence rate was 12.3% (n = 8). The survival rate at 5 years was 100% for TC and 87% for AC. Disease-free survival rates at 3 and 5 years were 95 and 93% for TC and 78 and 44% for AC, respectively (P = 0.004). Pathological nodal involvement (pN1-N2) did not affect overall survival or recurrence. CONCLUSIONS The surgical treatment of bronchial carcinoids provides high long-term survival rates. Low postoperative morbidity and mortality can be expected even after bronchial reconstruction. The AC appears to be the main factor that determines the risk of recurrence. Bronchial reconstructive lung sparing operations are not related to an increased recurrence rate.
Stochastic modelling based environment for synthesis and comparison of bus arbitration policies

This paper discusses a methodology to automatically design bus arbitration policies, and presents a comparison of different arbitration policies. Stochastic policies like randomized stochastic policy, deterministic policies, piecewise deterministic policies as well as some heuristic policies have been explored. We also discuss the extraction of data from the simulation models which has been used while implementing some of these policies. Modification of the policy generation methods to incorporate issues like fairness, starvation and deadlock prevention has also been discussed. We also discuss arbiter generation for a network processor system.
Silicon CMOS compatible in situ CCVD growth of graphene on silicon nitride

In this paper we report on the possibility of the silicon CMOS compatible fabrication of graphene field effect transistors on a silicon nitride high-k dielectric. For this purpose the catalytic chemical vapor deposition, which has already been approved to work on SiO2 surfaces [1], is used to grow graphene. First electrical results indicate a bilayer graphene with an on/off current ratio of 103 to 104, which can be achieved with lower threshold voltages. A greater on/off current ratio may be possible, as the off current is degraded through gate leakage current.
Transplantation of HGF gene-engineered skeletal myoblasts improve infarction recovery in a rat myocardial ischemia model

Background Skeletal myoblast transplantation seems a promising approach for the repair of myocardial infarction (MI). However, the low engraftment efficacy and impaired angiogenic ability limit the clinical efficiency of the myoblasts. Gene engineering with angiogenic growth factors promotes angiogenesis and enhances engraftment of transplanted skeletal myoblasts, leading to improved infarction recovery in myocardial ischemia. The present study evaluated the therapeutic effects of hepatocyte growth factor (HGF) gene-engineered skeletal myoblasts on tissue regeneration and restoration of heart function in a rat MI model. Methods and results The skeletal myoblasts were isolated, expanded, and transduced with adenovirus carrying the HGF gene (Ad-HGF). Male SD rats underwent ligation of the left anterior descending coronary artery. After 2 weeks, the surviving rats were randomized into four groups and treated with skeletal myoblasts by direct injection into the myocardium. The survival and engraftment of skeletal myoblasts were determined by real-time PCR and in situ hybridization. The cardiac function with hemodynamic index and left ventricular architecture were monitored; The adenovirus-mediated-HGF gene transfection increases the HGF expression and promotes the proliferation of skeletal myoblasts in vitro. Transplantation of HGF-engineered skeletal myoblasts results in reduced infarct size and collagen deposition, increased vessel density, and improved cardiac function in a rat MI model. HGF gene modification also increases the myocardial levels of HGF, VEGF, and Bcl-2 and enhances the survival and engraftment of skeletal myoblasts. Conclusions HGF engineering improves the regenerative effect of skeletal myoblasts on MI by enhancing their survival and engraftment ability.
A 280 ps - 7.5 ns UWB Pulse Generator with Amplitude Compensation in 40 nm CMOS

A novel highly flexible triangular pulse generator has been designed in 40 nm CMOS technology. The pulse width is adjustable between 280 ps an 7.5 ns. The generator has a maximum power consumption of 0.54 pJ/pulse from a 0.9V power supply. The pulse amplitude variation is compensated and is limited to 2.7 dB over the entire pulse width range. The triangular pulse is upconverted with a frequency mixer to generate a highly flexible ultra-wideband (UWB) pulse. To minimize the unwanted voltage controlled oscillator (VCO) leakage signal on the UWB pulse, the leakage of the frequency mixer is compensated by feedforward using a controlled mixer replica.
Learning compact hashing codes for efficient tag completion and prediction

Tags have been popularly utilized in many applications with image and text data for better managing, organizing and searching for useful information. Tag completion provides missing tag information for a set of existing images or text documents while tag prediction recommends tag information for any new image or text document. Valuable prior research has focused on improving the accuracy of tag completion and prediction, but limited research has been conducted for the efficiency issue in tag completion and prediction, which is a critical problem in many large scale real world applications. This paper proposes a novel efficient Hashing approach for Tag Completion and Prediction (HashTCP). In particular, we construct compact hashing codes for both data examples and tags such that the observed tags are consistent with the constructed hashing codes and the similarities between data examples are also preserved. We then formulate the problem of learning binary hashing codes as a discrete optimization problem. An efficient coordinate descent method is developed as the optimization procedure for the relaxation problem. A novel binarization method based on orthogonal transformation is proposed to obtain the binary codes from the relaxed solution. Experimental results on four datasets demonstrate that the proposed approach can achieve similar or even better accuracy with state-of-the-art methods and can be much more efficient, which is important for large scale applications.
Epitope Specificity Delimits the Functional Capabilities of Vaccine-Induced CD8 T Cell Populations

Despite progress toward understanding the correlates of protective T cell immunity in HIV infection, the optimal approach to Ag delivery by vaccination remains uncertain. We characterized two immunodominant CD8 T cell populations generated in response to immunization of BALB/c mice with a replication-deficient adenovirus serotype 5 vector expressing the HIV-derived Gag and Pol proteins at equivalent levels. The Gag-AI9/H-2Kd epitope elicited high-avidity CD8 T cell populations with architecturally diverse clonotypic repertoires that displayed potent lytic activity in vivo. In contrast, the Pol-LI9/H-2Dd epitope elicited motif-constrained CD8 T cell repertoires that displayed lower levels of physical avidity and lytic activity despite equivalent measures of overall clonality. Although low-dose vaccination enhanced the functional profiles of both epitope-specific CD8 T cell populations, greater polyfunctionality was apparent within the Pol-LI9/H-2Dd specificity. Higher proportions of central memory-like cells were present after low-dose vaccination and at later time points. However, there were no noteworthy phenotypic differences between epitope-specific CD8 T cell populations across vaccine doses or time points. Collectively, these data indicate that the functional and phenotypic properties of vaccine-induced CD8 T cell populations are sensitive to dose manipulation, yet constrained by epitope specificity in a clonotype-dependent manner.
Portosystemic collaterals in living donor liver transplantation: What is all the fuss about?

Portosystemic collaterals are a common finding in patients with cirrhosis undergoing liver transplantation. Recently, there has been a renewed interest regarding their significance in the setting of living donor liver transplantation (LDLT) due to concerns of graft hypoperfusion or hyperperfusion and its impact on early posttransplant outcomes. Presence of these collaterals has greater significance in the LDLT setting when compared with the deceased donor liver transplantation setting as dictated by the difference in the physiology of partial liver grafts. We discuss current thinking of portal flow dynamics and the techniques for dealing with this clinical problem. Liver Transplantation 23 537–544 2017 AASLD.
ABSORPTION OF HIGH ENERGY GAMMA-RAYS BY LOW ENERGY INTERGALACTIC PHOTONS

Following our previously proposed technique, we have used the recent-ray observations of Mkr421 to place theoretically signiicant constraints on and possible estimates of the intergalactic infrared radiation eld (IIRF). Our 2 upper limits and estimates are consistent with normal galactic IR production by stars and dust. They rule out exotic mechanisms proposed to produce a larger IIRF. We nd possible evidence for intergalactic absorption of-rays above 3 TeV energy in the observed spectrum of Mkr421. The implied IIRF is of the magnitude expected to be produced by stellar emission and reprocessing in galaxies. The sharpness of the spectral turnover is not consistent with the interpretation of this feature as a cutoo in the emission from the source. However, should the cutoo primarily be a result of absorption within the source itself, our possible extragalactic ux estimate becomes the strongest upper limit extant on the IIRF. Using models for the low energy intergalactic photon spectrum from microwave to ultraviolet energies, we calculate the opacity of intergalactic space to-rays as a function of energy and redshift. These calculations indicate that the GeV-ray burst recently observed by the CGRO EGRET detector originates at a redshift less than 1:5.
Multi-access channels with multiple decode-and-forward relays: Rate region and asymptotic sum-rate

This paper considers the Gaussian multiple access channel (MAC) assisted by N parallel relays. For the channel, the rate region with decode-and-forward is derived, considering both full-duplex and half-duplex relaying. The asymptotic sum-rate of the channel, under Rayleigh-distributed fading, is also presented. We prove that the sum-rate of the MAC with D&F relays converges almost surely to the sum-rate without relays. Hence, at the asymptote, multiuser diversity makes D&F relaying useless. Nevertheless, is also shown here that for finite number of users, the sum-rate converges to a strictly increasing function of the number of relays.
On the Power to Detect SNP/Phenotype Association in Candidate Quantitative Trait Loci Genomic Regions: A Simulation Study

We use coalescent methods to investigate the ability of linked neutral "markers" to reveal in simulated population samples the presence of one or more single nucleotide polymorphisms that is contributing to a trait having a complex genetic basis (QTN: quantitative trait nucleotide). Realistic mutation and recombination rates in our simulations allow us to generate SNP data appropriate for analyzing human variation across short chromosomal intervals corresponding to approximately 100 kilobases. We investigate the performance of both single marker and multiple-marker (haplotype) data for several ad hoc procedures. Our results with single SNP markers indicate that (1) the density of SNP markers need not be much higher than 10% in order to achieve near-maximal detection of a QTN; (2) a higher density of markers does not improve much on the ability to localize a QTN within an interval unless the recombination rate is high. Haplotype-based tests were investigated for the case in which more than one QTN is present in the studied interval. Larger sample sizes improve both the probability of detecting the haplotype with the largest number of QTNs, as well as the ability to infer correct haplotypes from genotypic data. Testing a series of short haplotypes across a longer interval can also be beneficial. The rate of false positives (i.e., when the most significant haplotype does not contain the greatest number of QTNs in the sample) can be very high when the contribution of individual QTNs to a trait is small. The elimination of low-frequency haplotypes does not substantially reduce the probability of detecting the haplotype with the largest number of QTNs but it can reduce the rate of false positives.
ON SEMIGROUPS WITH PSPACE-COMPLETE SUBPOWER MEMBERSHIP PROBLEM

Fix a finite semigroup $S$ and let $a_{1},\ldots ,a_{k},b$ be tuples in a direct power $S^{n}$ . The subpower membership problem (SMP) for $S$ asks whether $b$ can be generated by $a_{1},\ldots ,a_{k}$ . For combinatorial Rees matrix semigroups we establish a dichotomy result: if the corresponding matrix is of a certain form, then the SMP is in P; otherwise it is NP-complete. For combinatorial Rees matrix semigroups with adjoined identity, we obtain a trichotomy: the SMP is either in P, NP-complete, or PSPACE-complete. This result yields various semigroups with PSPACE-complete SMP including the six-element Brandt monoid, the full transformation semigroup on three or more letters, and semigroups of all $n$ by $n$ matrices over a field for $n\geq 2$ .