Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of Sex Chromosome Dosage Compensation in Animals: A Beautiful Theory, Undermined by Facts and Bedeviled by Details

Abstract Many animals with genetic sex determination harbor heteromorphic sex chromosomes, where the heterogametic sex has half the gene dose of the homogametic sex. This imbalance, if reflected in the abundance of transcripts or proteins, has the potential to deleteriously disrupt interactions between X-linked and autosomal loci in the heterogametic sex. Classical theory predicts that molecular mechanisms will evolve to provide dosage compensation that recovers expression levels comparable to ancestral expression prior to sex chromosome divergence. Such dosage compensating mechanisms may also, secondarily, result in balanced sex-linked gene expression between males and females. However, numerous recent studies addressing sex chromosome dosage compensation (SCDC) in a diversity of animals have yielded a surprising array of patterns concerning dosage compensation in the heterogametic sex, as well as dosage balance between sexes. These results substantially contradict longstanding theory, catalyzing both novel perspectives and new approaches in dosage compensation research. In this review, we summarize the theory, analytical approaches, and recent results concerning evolutionary patterns of SCDC in animals. We also discuss methodological challenges and discrepancies encountered in this research, which often underlie conflicting results. Finally, we discuss what outstanding questions and opportunities exist for future research on SCDC.
Diamond Sampling for Approximate Maximum All-Pairs Dot-Product (MAD) Search

Given two sets of vectors, A = {a1→, . , am→} and B = {b1→, . , bn→}, our problem is to find the top-t dot products, i.e., the largest |ai→ · bj→| among all possible pairs. This is a fundamental mathematical problem that appears in numerous data applications involving similarity search, link prediction, and collaborative filtering. We propose a sampling-based approach that avoids direct computation of all mn dot products. We select diamonds (i.e., four-cycles) from the weighted tripartite representation of A and B. The probability of selecting a diamond corresponding to pair (i, j) is proportional to (ai→ · bj→)2, amplifying the focus on the largest-magnitude entries. Experimental results indicate that diamond sampling is orders of magnitude faster than direct computation and requires far fewer samples than any competing approach. We also apply diamond sampling to the special case of maximum inner product search, and get significantly better results than the state-of-theart hashing methods.
Measurement Based Evaluation of the Wireless Identification and Sensing Platform

The Radio Frequency IDentification (RFID) technology has expanded rapidly and became very important during the last decades. New application are quickly emerging, as well as new protocols in order to reduce the identification process time. The Wireless Identification and Sensing Platform (WISP) was developed by Joshua R. Smith et al. in order to investigate RFID combined with computing and sensing applications. The WISP is an open source, open architecture EPCglobal conform RFID tag, operating in the Ultra High Frequency (UHF) band. It comprises a fully programmable low power 16 bit microcontroller, sensors and an energy harvesting stage that enables passive operation, i.e., the WISP is completely supplied by the electromagnetic field emitted by an RFID reader. To transport information from WISP to reader, the WISP modulates its antenna load impedance according to the data, thereby producing an amplitude-modulated backscatter signal that is captured by the reader. In this work, the properties of WISPs are investigated in order to determine their operational characteristics, implement new protocols and find out the characteristics of a multiple tag scenario. To that end, firmware for various application cases was written, radio frequency measurements were conducted and the results were evaluated. Through that course of action, some implementation obstacles were identified: considering several WISPs to be read out simultaneously, they have to be placed with a sufficient spacing, and synchronizing their responses remains a challenge.
**full Title** Asp Conference Series, Vol. **volume**, **year of Publication** **names of Editors** Planets of Young Stars

Since the first massive planet in a short period orbit was discovered, the question arised how such an object could have formed. There are basically two formation scenarios: migration due to planet-disk or planet-planet interaction. Which of the two scenarios is more realistic can be found out by observing short-period planets of stars with an age between 10 7 and 10 8 yrs. The second aim of the survey is to find out how many planets originally formed, and how many of these are destroyed in the first Gyrs: Do most young, close-in planets evaporate, or spiral into the host stars? In here we report on the first results of a radial-velocity search program for planets of young stars which we began in 2004. Using HARPS, we currently monitor 85 stars with ages between 10 7 and 10 8 yrs. We show that the detection of planets of young stars is possible. Up to now, we have identified 3 planet-candidates. Taking this result together with the results of other surveys, we conclude that the frequency of massive-short period planets of young stars is not dramatically higher than that of old stars. 1. The idea for the survey In the last 11 years, about 200 extrasolar planets have been detected indirectly by means of precise radial velocity (RV) surveys. The detection of now 16 transiting planets, as well as astrometric observations of ǫ Eri and the detection of the thermal emission of µ Andromeda b with the Spitzer satellite demonstrates that the vast majority of the objects found by RV-surveys are in fact planets (Charbonneau et al. The orbits of the extrasolar planets are surprisingly different from those in our solar system, as most of the long-period planets have rather eccentric orbits, and as there are planets with very short orbital periods (so called " hot Jupiters " , or " Pegasides " after the first such object found.). Up to now 49 extrasolar planets have been found which have a semi-major axis of ≤ 0.1 AU (orbital periods ≤ 10 days). When corrected for selection effects, the true frequency of hot Jupiters orbiting old stars is few % (Lineweaver & Grether, (2003)). The discovery of hot Jupiters was very surprising, and their formation still poses a mystery. In the standard model massive planets form via core accretion: In the first step a solid core of about 5 to 10 M …
A (In)Cast of Thousands: Scaling Datacenter TCP to Kiloservers and Gigabits

Abstract : This paper presents a practical solution to the problem of high-fan-in, high-bandwidth synchronized TCP workloads in datacenter Ethernets-the Incast problem. In these networks, receivers often experience a drastic reduction in throughput when simultaneously requesting data from many servers using TCP. Inbound data overfills small switch buffers, leading to TCP timeouts lasting hundreds of milliseconds. For many datacenter workloads that have a synchronization requirement (e.g., file system reads and parallel data intensive queries), incast can reduce throughput by up to 90%. Our solution for incast uses high-resolution timers in TCP to allow for microsecond-granularity timeouts. We show that this technique is effective in avoiding incast using simulation and real-world experiments. Last, we show that eliminating the minimum retransmission timeout bound is safe for all environments, including the wide-area.
Performance of Paced and Non-Paced Transmission Control Algorithms in Small Buffered Networks

Famous rule-of-thumb states that a buffer sized at B = RTT × BW, where RTT is the average round trip time and BW is the bandwidth of output link is necessary in order to achieve high utilization with TCP flows. However, as the link speeds continue increasing with technological advances, this buffer requirement starts becoming an important cost factor on routers of electronic networks. On the other hand, bursty nature of TCP limits further decreasing the buffer requirements, because it brings a high packet drop rate in small buffered networks. In this paper, we evaluate several transmission control algorithms in small buffered networks. The algorithms include TCP Reno, TCP NewReno, Highspeed TCP with SACK, and XCP. Simulation results show that all non-paced TCP and XCP variants perform poorly. Furthermore, the results show that even rule-of-thumb buffers are not enough for XCP in some cases because of high burstiness of XCP. We evaluate the effectiveness of pacing method at sender side for making transmission control algorithms suitable for very small buffered networks. We show that pacing alone is not enough for XCP to make suitable for small buffered networks, so we introduce a suitable parameter set. Simulation results show that buffer requirements on routers are greatly reduced by paced XCP with suitable parameter settings, while keeping the high fairness, fast convergence, and high utilization.
Associations of Endogenous Estradiol and Testosterone Levels With Plaque Composition and Risk of Stroke in Subjects With Carotid Atherosclerosis

Rationale: Sex steroids may play a role in plaque composition and in stroke incidence. Objectives: To study the associations of endogenous estradiol and testosterone with carotid plaque composition in elderly men and postmenopausal women with carotid atherosclerosis, as well as with risk of stroke in this population. Methods and Results: Data of 1023 postmenopausal women and 1124 men (≥45 years) with carotid atherosclerosis, from prospective population-based RS (Rotterdam Study), were available. At baseline, total estradiol (TE) and total testosterone (TT) were measured. Carotid atherosclerosis was assessed by ultrasound, whereas plaque composition (presence of calcification, lipid core, and intraplaque hemorrhage) was assessed by magnetic resonance imaging. TE and TT were not associated with calcified carotid plaques in either sex. TE was associated with presence of lipid core in both sexes (in women odds ratio, 1.48 [95% confidence interval [CI], 1.02–2.15]; in men odds ratio, 1.23 [95% CI, 1.03–1.46]), whereas no association was found between TT and lipid core in either sex. Higher TE (odds ratio, 1.58 [95% CI, 1.03–2.40]) and lower TT (odds ratio, 0.82 [95% CI, 0.68–0.98]) were associated with intraplaque hemorrhage in women but not in men. In women, TE was associated with increased risk of stroke (hazard ratio, 1.98 [95% CI, 1.01–3.88]), whereas no association was found in men. TT was not associated with risk of stroke in either sex. Conclusions: TE was associated with presence of vulnerable carotid plaque as well as increased risk of stroke in women, whereas no consistent associations were found for TT in either sex.
Thermal stability studies of a globular protein in aqueous poly(ethylene glycol) by 1H NMR

The reversible folding destabilization of hen lysozyme has been confirmed by a melting temperature (Tm) decrease in aqueous poly(ethylene glycol) (PEG). The percent denatured, extracted from the histidine 15 C2H (H15 C2H) native and denatured peak areas from 500‐MHz one‐dimensional proton nuclear magnetic resonance (1D 1H NMR) spectra in D2O, was analyzed through denaturation temperatures at 0% and 20% (w/w) PEG 1000. The lysozyme (3.5 mM) Tm decreased by 4.2°C and 7.1°C in 20% (w/w) PEG 1000 at pH 3.8 and 3.0, respectively. The Tm decreased with increasing lysozyme concentration. Additionally, the temperature‐induced resonance migrations of 17 protons from 8 residues indicate that the native lysozyme structure undergoes temperature‐induced conformational changes. The changes were essentially identical in both 0% and 20% (w/w) PEG 1000 at both pH 3.0 and 3.8. This small, local restructuring of the hydrophobic box region may be a manifestation of temperature‐dependent solution hydrophobicity, whereas active‐site cleft fluctuations may be due to the inherent active‐site flexibility. The lysozyme structure in PEG at 35°C was determined to be essentially native from the 1H nuclear Overhauser effect spectroscopy (NOESY) fingerprint regions. Additionally, lysozyme chemical shifts, from 1D spectra, in PEG 200, 300, and 1000 at 35°C and various concentrations were essentially identical, further confirming that the conformation remains native in various PEG solutions. © 1996 John Wiley & Sons, Inc.
Sound Source Localization in a Multipath Environment Using Convolutional Neural Networks

The propagation of sound in a shallow water environment is characterized by boundary reflections from the sea surface and sea floor. These reflections result in multiple (indirect) sound propagation paths, which can degrade the performance of passive sound source localization methods. This paper proposes the use of convolutional neural networks (CNNs) for the localization of sources of broadband acoustic radiated noise (such as motor vessels) in shallow water multipath environments. It is shown that CNNs operating on cepstrogram and generalized cross-correlogram inputs are able to estimate more reliably the instantaneous range and bearing of transiting motor vessels when the source localization performance of conventional passive ranging methods is degraded. The ensuing improvement in source localization performance is demonstrated using real data collected during an at-sea experiment.
Ovarian endometriosis: from pathogenesis to surgical treatment

Purpose of review This review analyzes the literature on ovarian endometrioma, examining the controversies on pathogenesis, malignant transformation and surgical therapy. Recent findings Recent literature reflects the necessity of clearly defining the ethiologic and pathologic factors that determine the origin of ovarian endometriosis and explain the increase in the condition with the prospect of developing effective prevention therapy. The possibility that ovarian endometriomas undergo malignant transformation is widely reported in the literature. Recent studies underline the importance of detecting histological differences in endometriosis (hyperplasia and atypia) and several studies of molecular biology support the theory of genetic alterations interfering with malignant transformation of ovarian endometriosis. Summary The surgical approach must take into account all this information and, when the therapy is conservative, complete excision of the disease must be laparoscopically performed without affecting the healthy ovarian tissue.
Social Implications of Smartphone Use: Korean College Students' Smartphone Use and Psychological Well-Being

The purpose of this study is to explore the relationship between motives of smartphone use, social relation, and psychological well-being. The correlation analysis shows that the motives of smartphone use were positively related to bonding relations but negatively related to bridging relations. The hierarchical multiple regression analysis finds the associations among motives of smartphone use, social relations, perceived social support, and variables of psychological well-being. The results demonstrate that needs for caring for others were negatively related to loneliness and depression and positively related to self-esteem. However, the communication motives are not a significant predictor to determine self-esteem, loneliness, and depression. In addition, bonding and bridging social relations and social support significantly increase self-esteem and decrease loneliness and depression.
On the role of subgrid-scale coherent modes in large-eddy simulation

The role of coherent and incoherent subgrid-scale modes in large-eddy simulation modelling is examined. The coherent/incoherent decomposition of the subgrid-scale stresses based on the wavelet de-noising procedure is introduced. A priori dynamical tests based on the perfect modelling approach are performed for decaying isotropic turbulence. The theoretical effects of coherent and incoherent subgrid-scale forces are dynamically evaluated during the simulation. The relation between deterministic/stochastic subgrid-scale models and coherent/incoherent subgrid-scale stresses is discussed. The main result is that in large-eddy simulations low-order statistics can be almost exactly reproduced when only the effect of the coherent subgrid-scale modes is accounted for, while the incoherent subgrid-scale modes have a negligible effect upon the large-scale dynamics and the energy transfer.
Dual-CCD Complete Stokes Simultaneously Imaging Polarimeter and Experimental Data Analysis

Polarization imaging technology that is on the basis of the polarization measurement can change the obtained polarization information into two-dimensional image, from which we can acquire polarization characteristics of target scene just like normal gray image so that this technique is widely used in the fields of military investigation, medical testing, space exploration, meteorology and so on. Traditional imaging polarimeter is time sequence polarization imaging, which is to use sequential rotational polarization components (line polarizer or wave plate etc.) and to combine Fourier analysis method to acquire final Stokes components. But because of the sacrificing of temporal resolution, this technique does not meet the needs of the situation of high-speed dynamic changing scene. While current simultaneously polarization imaging technique commonly uses multiple sets of optical systems and at least four CCD cameras, which have the problems of low energy utilization rate and non-matching performance among the optical sets. To solve the aforementioned problems, we design and implement a set of non-mechanical rotating parts, double Wollaston prisms-based high resolution simultaneously imaging polarimeter. This system uses the specific combination of non-polarizing beam splitter, Wollaston prisms and wave plates to divide the incident target space beam into four optical paths of different polarization states which can be taken into two types: two paths in the reflection part and two paths in the transmission part. Finally the imaging lens converge the beam to different regions of two large array CCD to image four images. To achieve the goal of extracting complete Stokes information, we apply the Stokes vector and Mueller matrix analysis. The article presents systems structure, working theory, calibration method, experiment data analysis and system polarization performance, which provides a good reference for the simultaneously high-speed polarization imaging.
Two Distinct Functional Patterns of Hepatitis C Virus (HCV)-Specific T Cell Responses in Seronegative, Aviremic Patients

In hepatitis C Virus (HCV) high-risk groups, HCV-specific T cell responses have been detected in seronegative, aviremic persons who have no evidence of HCV infection. Herein, we investigated functional profiles of HCV-specific T-cell responses in seronegative, aviremic patients of a HCV high-risk group. Seventy seven hemodialysis patients with chronic renal disease were analyzed by IFN-γ ELISpot assays, and eight of 71 (11.3%) seronegative, aviremic patients displayed HCV-specific T-cell responses. Their HCV-specific memory T cells were characterized by assessing cytokine polyfunctionality, known to provide antiviral protection. By intracellular staining of IFN-γ, TNF-α, IL-2 and MIP-1β, we identified two distinct populations in the seronegative, aviremic patients: polyfunctional responders and TNF-α-predominant responders. In further analysis, occult HCV infection was excluded as a cause of the HCV-specific T cell response via secondary nested RT-PCR of HCV RNA in peripheral blood mononuclear cell samples. HCV-specific T cells targeted multiple epitopes including non-structural proteins in a single patient, implying that their T cells might have been primed by HCV proteins synthesized within the host. We conclude that HCV-specific memory T cells of seronegative, aviremic patients arise from authentic HCV replication in the host, but not from current occult HCV infection. By functional pattern of HCV-specific T cells, there are two distinct populations in these patients: polyfunctional responders and TNF-α-predominant responders.
Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes

The plastid genomes of several plants contain homologues, termed ndh genes, of genes encoding subunits of the NADH:ubiquinone oxidoreductase or complex I of mitochondria and eubacteria. The functional significance of the Ndh proteins in higher plants is uncertain. We show here that tobacco chloroplasts contain a protein complex of 550 kDa consisting of at least three of the ndh gene products: NdhI, NdhJ and NdhK. We have constructed mutant tobacco plants with disrupted ndhC, ndhK and ndhJ plastid genes, indicating that the Ndh complex is dispensible for plant growth under optimal growth conditions. Chlorophyll fluorescence analysis shows that in vivo the Ndh complex catalyses the post‐illumination reduction of the plastoquinone pool and in the light optimizes the induction of photosynthesis under conditions of water stress. We conclude that the Ndh complex catalyses the reduction of the plastoquinone pool using stromal reductant and so acts as a respiratory complex. Overall, our data are compatible with the participation of the Ndh complex in cyclic electron flow around the photosystem I complex in the light and possibly in a chloroplast respiratory chain in the dark.
Stimulating PD-1–negative signals concurrent with blocking CD154 co-stimulation induces long-term islet allograft survival1

Background. A balanced network of positive and negative T-cell co-stimulatory signals is important in regulating T-cell activation. Blocking CD28, CD154 (CD40L), or both co-stimulatory molecules has been efficacious in preventing acute allograft rejection in certain but not all transplantation models. In the present study, the authors tested the hypothesis that stimulating programmed death 1 (PD-1)–triggered negative signals concurrent with blocking CD154 co-stimulatory signals would facilitate islet allograft tolerance. Methods. The authors used a dimeric PD-L1 immunoglobulin (Ig) fusion protein to stimulate the inhibitory receptor PD-1, and a monoclonal antibody to block CD154. The effects of PD-1 engagement and CD154 blockade on lymphocyte activation were determined by cell proliferation, flow cytometry, and a model of islet transplantation. Results. PD-L1Ig inhibited the proliferation of both CD4+ and CD8+ T cells stimulated by anti-CD3. The inhibitory effect of PD-L1Ig was enhanced by concurrent blockade of CD154 co-stimulatory signals, as demonstrated by T-cell proliferation and expression of cell surface activation markers. PD-L1Ig and anti-CD154 also synergistically blocked the activation and maturation of antigen-presenting cells. In an islet transplantation model, treatment of recipient C57BL/6 (H-2b) mice with PD-L1Ig and anti-CD154 induced long-term survival of DBA/2 (H-2d) islet allografts, whereas treatment with each reagent alone failed to prevent islet allograft rejection. Conclusions. These results suggest that engaging the negative receptor PD-1 exhibits critical immunoregulatory effects in the allograft response, and blocking positive co-stimulatory molecules with active delivery of inhibitory signals may represent a novel therapeutic strategy in transplantation.