Miracle-dz/UniFAR-FTUs huggingface dataset:
An Assessment of the Impacts of Molecular Oxygen on the Evolution of Proteomes

Oxygen is not only one of life's essential elements but also a source of protein damage, mutagenesis, and ageing. Many proteome adaptations have been proposed to tackle such stresses and we assessed them using comparative genomics in a phylogenetic context. First, we find that aerobiosis is a trait with important phylogenetic inertia but that oxygen content in proteins is not. Instead, oxygen content is close to the expected values given the nucleotide composition. Accordingly, we find no evidence of oxygen being a scarce resource for protein synthesis even among anaerobes. Second, we searched for counterselection of amino acids more prone to oxidation among aerobes. Only cysteine follows the expected trend, whereas tryptophan follows the inverse one. When analyzing composition in the context of protein structures and residue accessibility, we find that all oxidable residues are avoided at the surface of proteins. Yet, there is no difference between aerobes and anaerobes in this respect, and the effect might be explained by the hydrophobicity of these residues. Third, we revisited the hypothesis that atmospheric enrichment in molecular oxygen led to the development of the communication capabilities of eukaryotes. With a larger data set and adequate controls, we confirm the trend of longer oxygen-rich outer domains in transmembrane proteins of eukaryotes. Yet, we find no significant association between oxygen concentration in the environment and this trait within prokaryotes, suggesting that this difference is clade specific and independent of oxygen availability. We find that genes involved in cellular responses to oxygen are much more frequent among aerobes, and we suggest that they erase most expected differences in terms of proteome composition between organisms facing high and low oxygen concentrations.
Multicenter clinical assessment of improved wearable multimodal convulsive seizure detectors

New devices are needed for monitoring seizures, especially those associated with sudden unexpected death in epilepsy (SUDEP). They must be unobtrusive and automated, and provide false alarm rates (FARs) bearable in everyday life. This study quantifies the performance of new multimodal wrist‐worn convulsive seizure detectors.
Glycosylation at Asn211 Regulates the Activation State of the Discoidin Domain Receptor 1 (DDR1)

Background: DDR1 is a receptor tyrosine kinase that signals in response to collagen. Results: Mutagenesis at the 211NDS glycosylation site enhances receptor dimerization and results in ligand-independent receptor autophosphorylation. Conclusion: N-Glycosylation of DDR1 plays a critical role in maintenance of the inactive state of the receptor dimers. Significance: These studies highlight a new structural feature that regulates DDR1 activation. Discoidin domain receptor 1 (DDR1) belongs to a unique family of receptor tyrosine kinases that signal in response to collagens. DDR1 undergoes autophosphorylation in response to collagen binding with a slow and sustained kinetics that is unique among members of the receptor tyrosine kinase family. DDR1 dimerization precedes receptor activation suggesting a structural inhibitory mechanism to prevent unwarranted phosphorylation. However, the mechanism(s) that maintains the autoinhibitory state of the DDR1 dimers is unknown. Here, we report that N-glycosylation at the Asn211 residue plays a unique role in the control of DDR1 dimerization and autophosphorylation. Using site-directed mutagenesis, we found that mutations that disrupt the conserved 211NDS N-glycosylation motif, but not other N-glycosylation sites (Asn260, Asn371, and Asn394), result in collagen I-independent constitutive phosphorylation. Mass spectrometry revealed that the N211Q mutant undergoes phosphorylation at Tyr484, Tyr520, Tyr792, and Tyr797. The N211Q traffics to the cell surface, and its ectodomain displays collagen I binding with an affinity similar to that of the wild-type DDR1 ectodomain. However, unlike the wild-type receptor, the N211Q mutant exhibits enhanced receptor dimerization and sustained activation upon ligand withdrawal. Taken together, these data suggest that N-glycosylation at the highly conserved 211NDS motif evolved to act as a negative repressor of DDR1 phosphorylation in the absence of ligand. The presence of glycan moieties at that site may help to lock the collagen-binding domain in the inactive state and prevent unwarranted signaling by receptor dimers. These studies provide a novel insight into the structural mechanisms that regulate DDR activation.
Temporal and Spatial Enumeration Processes in the Primate Parietal Cortex

Humans and animals can nonverbally enumerate visual items across time in a sequence or rapidly estimate the set size of spatial dot patterns at a single glance. We found that temporal and spatial enumeration processes engaged different populations of neurons in the intraparietal sulcus of behaving monkeys. Once the enumeration process was completed, however, another neuronal population represented the cardinality of a set irrespective of whether it had been cued in a spatial layout or across time. These data suggest distinct neural processing stages for different numerical formats, but also a final convergence of the segregated information to form most abstract quantity representations.
Empagliflozin as Add-On to Metformin in Patients With Type 2 Diabetes: A 24-Week, Randomized, Double-Blind, Placebo-Controlled Trial

OBJECTIVE To investigate the efficacy and tolerability of empagliflozin as an add-on to metformin therapy in patients with type 2 diabetes. RESEARCH DESIGN AND METHODS Patients with HbA1c levels of ≥7% to ≤ 10% (≥53 to ≤86 mmol/mol) while receiving metformin (≥1,500 mg/day) were randomized and treated with once-daily treatment with empagliflozin 10 mg (n = 217), empagliflozin 25 mg (n = 213), or placebo (n = 207) for 24 weeks. The primary end point was the change in HbA1c level from baseline at week 24. Key secondary end points were changes from baseline in weight and mean daily glucose (MDG) at week 24. RESULTS At week 24, adjusted mean (SE) changes from baseline in HbA1c were −0.13% (0.05)% (−1.4 [0.5] mmol/mol) with placebo, −0.70% (0.05)% (−7.7 [0.5] mmol/mol) with empagliflozin 10 mg, and −0.77% (0.05)% (−8.4 [0.5] mmol/mol) with empagliflozin 25 mg (both P < 0.001). Empagliflozin significantly reduced MDG level and systolic and diastolic blood pressure (BP) versus placebo. Adjusted mean (SE) changes from baseline in weight were −0.45 kg (0.17 kg) with placebo, −2.08 kg (0.17 kg) with empagliflozin 10 mg, and −2.46 kg (0.17 kg) with empagliflozin 25 mg (both P < 0.001). Adverse events (AEs) were similar across groups (placebo 58.7%; empagliflozin 49.5–57.1%). Confirmed hypoglycemic AEs were reported in 0.5%, 1.8%, and 1.4% of patients receiving placebo, empagliflozin 10 mg, and empagliflozin 25 mg, respectively. Events consistent with urinary tract infections were reported in 4.9%, 5.1%, and 5.6% of patients, and events consistent with genital infections were reported in 0%, 3.7%, and 4.7% of patients, respectively. CONCLUSIONS Empagliflozin 10 and 25 mg for 24 weeks as add-on to metformin therapy significantly improved glycemic control, weight, and BP, and were well-tolerated.
First in the family: how high-achieving, first-generation Vietnamese-American students navigate the elite college environment, a study using portraiture methodology.

First in the family: how high-achieving, first-generation Vietnamese-American students navigate the elite college environment, a study using portraiture methodology, is an in-depth study of five Vietnamese-American students at an elite institution, Ivy College (pseudonym). The main purpose of the study was to examine the lived experiences of first-generation VietnameseAmerican students at a highly selective college using Portraiture methodology. The study analyzed the data using Bourdieuian’s theory of social and cultural capital. The main research questions were: (1) What does being first-generation mean for Vietnamese-American students at Ivy College? (2) What challenges do first-generation Vietnamese-American students experience at Ivy College? (3) How do Vietnamese-American students navigate the elite college environment? Findings from the study indicated that first-generation Vietnamese-American students are able to navigate the elite college environment; however, they had to overcome daunting obstacles. Consistent with extant research, certain characteristics of first-generation, low-income students were evidenced. Participants in the study reported that their parents were extremely supportive of their children’s education, even though their parents were not able to help them navigate the college application process and eventual matriculation. All participants experienced significant challenges in college due to their lack of social and cultural capital, lowincome status, and first-generation status.
Androgen receptor mitigates postoperative disease progression of hepatocellular carcinoma by suppressing CD90+ populations and cell migration and by promoting anoikis in circulating tumor cells

Purpose Although hepatectomy and liver transplantation surgery for hepatocellular carcinoma (HCC) are effective treatment modalities, the risk of recurrence remains high, particularly in patients with a high number of circulating tumor cells (CTCs) expressing cancer stem/progenitor cell markers. Androgen receptor (AR) signaling has been shown to suppress HCC metastasis in rodent models of HCC. In this study, we investigated whether AR is associated with postoperative HCC recurrence. Experimental Design CTCs were obtained from patients with HCC who had undergone hepatectomy to investigate whether they are associated with disease outcome. AR knockout was introduced in two mouse models of spontaneous HCC (carcinogen- and hepatitis B virus-related HCC) to delineate the role that AR plays in HCC recurrence. Biological systems analysis was used to investigate the cellular and molecular mechanisms. Results We found that the expression of AR in CTCs was negatively associated with HCC recurrence/progression after hepatectomy. Our results suggest that AR-mediated suppression of HCC recurrence/progression is governed by a three-pronged mechanism. First, AR suppresses the expression of CD90 in CTCs by upregulating Histone 3H2A. Second, AR suppresses cell migration at the transcriptome level. Third, AR promotes anoikis of CTCs via dysregulation of cytoskeletal adsorption. Conclusions The results indicate that AR expression may be the gatekeeper of postoperative HCC recurrence. Therefore, targeting AR in presurgical down-staging procedures may serve as a secondary prevention measure against HCC recurrence in the future.
Exploring Performance and Power Scaling in Multi-Core Processors

The demand for lower power over higher performance processors has increased over the past few years, leading to multi-core architectures. The current trend being favoring few powerful cores over a larger number of simpler, smaller cores. We address the tradeo between these two design decisions by considering Pollack’s Rule for single cores and applying it with Amdahl’s law to multi-core architectures. We use McPAT to obtain power and area data for cores with varying pipeline widths, then gather performance data of the cores from the M5 simulator and SPEC2006 benchmarks. For all congurations tested, given either a power or area budget, a processor consisting of a moderate number of medium-sized cores gives the best overall performance-per-watt.
Performance and Feasibility Study of a Standing Column Well (SCW) System Using a Deep Geothermal Well

Deep geothermal heat pump systems have considerable energy saving potential for heating and cooling systems that use stable ground temperature and groundwater as their heat sources. However, deep geothermal systems have several limitations for real applications such as a very high installation cost and a lack of recognition as heating and cooling systems. In this study, we performed a feasibility assessment of a Standing Column Well (SCW) system using a deep geothermal well, based on a real-scale experiment in Korea. The results showed that the temperature of the heat source increased up to 42.04 °C in the borehole after the heating experiment, which is about 30 °C higher than that of normal shallow geothermal wells. Furthermore, the coefficient of performance (COP) of the heat pump during 3 months of operation was 5.8, but the system COP was only 3.6 due to the relatively high electric consumption of the pump. Moreover, the payback period of the system using a deep well for controlled horticulture in a glass greenhouse was calculated as 6 years compared with using a diesel boiler system.
Is it worth to be patient? Analysis and optimization of delayed mobile data offloading

Operators have recently resorted to WiFi offloading to deal with increasing data demand and induced congestion. Researchers have further suggested the use of “delayed offloading”: if no WiFi connection is available, (some) traffic can be delayed up to a given deadline, or until WiFi becomes available. Nevertheless, there is no clear consensus as to the benefits of delayed offloading, with a couple of recent experimental studies largely diverging in their conclusions. Nor is it clear how these benefits depend on network characteristics (e.g. WiFi availability), user traffic load, etc. In this paper, we propose a queueing analytic model for delayed offloading, and derive the mean delay, offloading efficiency, and other metrics of interest, as a function of the user's “patience”, and key network parameters. We validate the accuracy of our results using a range of realistic scenarios, and use these expressions to show how to optimally choose deadlines.
The Meso-Structured Magnetic Atmosphere -- A Stochastic Polarized Radiative Transfer Approach

We present a general radiative transfer model which allows the Zeeman diagnostics of complex and unresolved solar magnetic fields. Present modeling techniques still rely to a large extent on a-priori assumptions about the geometry of the underlying magnetic field. In an effort to obtain a more flexible and unbiased approach we pursue a rigorous statistical description of the underlying atmosphere. Based on a Markov random field model the atmospheric structures are characterized in terms of probability densities and spatial correlations. This approach allows us to derive a stochastic transport equation for polarized light valid in a regime with an arbitrary fluctuating magnetic field on finite scales. One of the key ingredients of the derived stochastic transfer equation is the correlation length which provides an additional degree of freedom to the transport equation and can be used as a diagnostic parameter to estimate the characteristic length scale of the underlying magnetic field. It is shown that the stochastic transfer equation represents a natural extension of the (polarized) line formation under the micro- and macroturbulent assumption and contains both approaches as limiting cases. In particular, we show how in an inhomogeneous atmosphere asymmetric Stokes profiles develop and that the correlation length directly controls the degree of asymmetry and net circular polarization (NCP). In a number of simple numerical model calculations we demonstrate the importance of a finite correlation length for the polarized line formation and its impact on the resulting Stokes line profiles.
Association Between Glycemic Control and Morning Blood Pressure Surge With Vascular Endothelial Dysfunction in Type 2 Diabetic Patients

OBJECTIVE Morning blood pressure surge (MBPS) is an independent predictor of cardiovascular events. However, little is known about the association between glycemic control and MBPS, and its effect on vascular injury in patients with type 2 diabetes mellitus (T2DM). The current study examined the association between glycemic control and MBPS, and the involvement of MBPS in the development of vascular dysfunction in T2DM patients. RESEARCH DESIGN AND METHODS We examined MBPS in T2DM patients (25 male patients/25 female patients; mean age, 60.1 ± 13.2 years; n = 50) using 24-h ambulatory blood pressure monitoring, and assessed vascular function by brachial artery flow-mediated dilation (FMD) and nitroglycerin-mediated dilation (NMD). RESULTS HbA1c (ρ = 0.373, P = 0.009) and triglyceride (TG) (ρ = 0.375, P = 0.009) levels correlated significantly and positively with MBPS. In multiple regression analysis, including TG and HbA1c levels in addition to age and 24-h systolic blood pressure (SBP) as independent variables, HbA1c (β = 0.328, P = 0.016) and TG (β = 0.358, P = 0.014) were associated significantly in a positive manner with MBPS. In a noninsulin user, when homeostasis model assessment ratio (HOMA-R) was included in place of TG, HOMA-R emerged as a significant factor. MBPS (ρ = −0.289, P = 0.043) and HbA1c (ρ = −0.301, P = 0.035) correlated significantly and negatively with FMD, whereas 24-h SBP correlated with both FMD (ρ = −0.359, P = 0.012) and NMD (ρ = −0.478, P = 0.004). In multiple regression analysis, including age, gender, 24-h SBP, MBPS, LDL cholesterol, and HbA1c, MBPS (β = −0.284, P = 0.044) alone associated significantly in a negative manner with FMD, but not with NMD. CONCLUSIONS The current study demonstrated that poor glycemic control and insulin resistance are independently associated with the occurrence of MBPS in T2DM patients, which might be significantly associated with endothelial dysfunction.
Spike-Time Dependant Plasticity in a Spiking Neural Network for Robot Path Planning

Abstract. This paper will present a path planning technique for autonomous mobile robot, based on the representation of the environment as a cognitive map through a spiking neural network (SNN) of O’Keefe place cells. The method is based on the concept of the travelling wave. For this purpose, we use a biologically plausible neural model (Izhikevitch model) which is the medium of a travelling wavefront stabilized by the Spike-Time Dependant Plasticity (STDP) process. The obstacles are represented by inhibited neurons and the robot by the unique externally excited place cell that initiates the wave. This method produces a gradient map that allows fast and reliable calculation of a feasible path.
Hand Gesture Recognition Based on Perceptual Shape Decomposition with a Kinect Camera

SUMMARY In this paper, we propose the Perceptual Shape Decompo-sition (PSD) to detect ﬁngers for a Kinect-based hand gesture recognitionsystem. The PSD is formulated as a discrete optimization problem by re-moving all negative minima with minimum cost. Experiments show thatour PSD is perceptually relevant and robust against distortion and handvariations, and thus improves the recognition system performance. key words: Kinect camerta, hand gesture recognition, perceptual decom-position, ﬁnger detection 1. Introduction Hand gesture recognition is important for human-computerinteraction (HCI) in diﬀerent areas, such as virtual reality,signlanguagerecognition,andcomputergames[1]. Usuallythe shape feature is suﬃcient for successful recognition[2]. However, due to the nature of optical sensor, the quality ofcaptured images is sensitive to the lighting conditions andcluttered backgrounds, which makes it very diﬃcult to ob-tain hand shapes[3]. Thanks to the recent advent of the Kinect depth cam-era[4], new opportunities for hand gesture recognitionemerge. Ren et al. were the ﬁrst to develop a real-lifehand gesture recognition system with a Kinect sensor[5],as shown in Fig.1. With the assistant of depth cue, theirsystem can segment hands robustly. However, due to thelow-resolutionoftheKinectdepthmapandthesmallsizeofhand image, the segmentation of hand is usually inaccurateand noisy, which signiﬁcantly aﬀects the recognition per-formance. In order to address this problem, they proposedthe Finger-Earth Mover’s Distance (FEMD), which onlymatches the ﬁngers rather than the whole hand[5]. Thus,the ﬁnger detection has a signiﬁcant impact upon robust-ness, accuracy and eﬃciency of their hand gesture recogni-tion system.Ren et al. presented two shape decomposition meth-ods for ﬁnger detection. The ﬁrst one is the Threshold-ing Decomposition (TD)[6]. This method decomposes out-stretched ﬁngers using a circle that is concentric with themaximal inscribed circle of the hand shape and of radiusa speciﬁed threshold value. Despite the implementation
Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Stochastic rearrangement of germline V-, D-, and J-genes to create variable coding sequence for certain cell surface receptors is at the origin of immune system diversity. This process, known as “VDJ recombination”, is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Because any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on nonproductive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our probabilistic model predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.
When Demand Creates its Own Supply: Saving Traps

The mechanism by which aggregate supply creates the income that generates its matching demand (called Say's Law), may not work in a general equilibrium with decentralized markets and savings in bonds or money. Full employment is an equilibrium, but convergence to that state is slow. A self-fulfilling precautionary motive to accumulate bonds (with a zero aggregate supply) can set the economy on an equilibrium path with a fast convergence towards a steady state with unemployment that may be an absorbing state from which no equilibrium path emerges to restore full employment.
A decidable weakening of Compass Logic based on cone-shaped cardinal directions

We introduce a modal logic, called Cone Logic, whose formulas describe properties of points in the plane and spatial relationships between them. Points are labelled by proposition letters and spatial relations are induced by the four cone-shaped cardinal directions. Cone Logic can be seen as a weakening of Venema's Compass Logic. We prove that, unlike Compass Logic and other projection-based spatial logics, its satisfiability problem is decidable (precisely, PSPACE-complete). We also show that it is expressive enough to capture meaningful interval temporal logics - in particular, the interval temporal logic of Allen's relations "Begins", "During", and "Later", and their transposes.