Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Different T Cell Receptors in the Development of Pre–T Cells

The development of pre–T cells with productive TCR-β rearrangements can be mediated by each the pre–T cell receptor (pre-TCR), the TCR-αβ as well as the TCR-γδ, albeit by distinct mechanisms. Although the TCR-γδ affects CD4−8− precursor cells irrespective of their rearrangement status by TCR-β mechanisms not involving TCR-β selection, both the preTCR and the TCR-αβ select only cells with productive TCR-β genes for expansion and maturation. The TCR-αβ appears to be much less effective than the pre-TCR because of the paucity of TCR-α proteins in TCR-β–positive precursors since an early expressed transgenic TCR-αβ can largely substitute for the pre-TCR. Thus, the TCR-αβ can assume a role not only in the rescue from programmed cell death of CD4+8+ but also of CD4−8− thymocytes. In evolution this double function of the TCR-αβ may have been responsible for the maturation of αβ T cells before the advent of the pre–TCR-α chain.
Blockwise SVD with error in the operator and application to blind deconvolution

We consider linear inverse problems in a nonparametric statistical framework. Both the signal and the operator are unknown and subject to error measurements. We establish minimax rates of convergence under squared error loss when the operator admits a blockwise singular value decomposition (blockwise SVD) and the smoothness of the signal is measured in a Sobolev sense. We construct a nonlinear procedure adapting simultaneously to the unknown smoothness of both the signal and the operator and achieving the optimal rate of convergence to within logarithmic terms. When the noise level in the operator is dominant, by taking full advantage of the blockwise SVD property, we demonstrate that the block SVD procedure outperforms classical methods based on Galerkin projection or nonlinear wavelet thresholding. We subsequently apply our abstract framework to the specific case of blind deconvolution on the torus and on the sphere.
Ocular imaging of attentional bias among college students: automatic and controlled processing of alcohol-related scenes.

OBJECTIVE Heavy episodic drinking in college is an issue of major concern in our society. In the college setting, where alcohol misuse is prevalent, alcohol-related perceptions and automatic attentional biases may be important determinants in students' decisions to engage in risking drinking behaviors. The current study examined college students' attention to alcohol-related beverages in real time using ocular-imaging techniques. The authors hypothesized that alcohol-consumption characteristics such as quantity-frequency of alcohol consumption would predict ocular-imaging indices of attentional bias to alcohol-related images. METHOD Twenty-six college students successfully completed questionnaires assessing basic demographics and alcohol-consumption characteristics, followed by an eye-tracking task in which they viewed pictorial stimuli consisting of photographs of alcohol-related scenes, household objects, or a combination of these items. RESULTS Quantity-frequency index (QFI) of alcohol consumption was positively related to the percentage of initial ocular fixations on the alcohol-related items (r = .62, p = .001), whereas QFI negatively predicted the percentage of initial ocular fixations on the control images (r = -.60, p = .002). In addition, QFI positively predicted participants' dwell time on alcohol-related images (r = .57, p = .005), and negatively predicted dwell time on control images (r = -.41, p = .05). Age at first drink and days since last alcohol consumption were not related to eye-tracking metrics. CONCLUSIONS Ocular-imaging methods are a valuable tool for use in the study of attentional bias to alcohol-related images in college drinkers. Further research is needed to determine the potential application of these methods to the prevention and treatment of alcohol misuse on college campuses.
Ethernet: distributed packet switching for local computer networks

Ethernet is a branching broadcast communication system for carrying digital data packets among locally distributed computing stations. The packet transport mechanism provided by Ethernet has been used to build systems which can be viewed as either local computer networks or loosely coupled multiprocessors. An Ethernet's shared communication facility, its Ether, is a passive broadcast medium with no central control. Coordination of access to the Ether for packet broadcasts is distributed among the contending transmitting stations using controlled statistical arbitration. Switching of packets to their destinations on the Ether is distributed among the receiving stations using packet address recognition. Design principles and implementation are described based on experience with an operating Ethernet of 100 nodes along a kilometer of coaxial cable. A model for estimating performance under heavy loads and a packet protocol for error controlled communication are included for completeness.
A Flocking Boids Simulation and Optimization Structure for Mobile Multicore Architectures

During the past few years, mobile phones and other mobile devices have gone from simple phone and messaging devices to high end smartphones with serious computing capabilities. Nowadays, most of these devices are equipped with multicore processors like dual- core CPUs and GPUs, which are designed for both low power consumption and high performance computation. Moreover, most devices still lack libraries for generic multicore computing usage, such as CUDA or OpenCL. However, computing certain specific kind of tasks in these mobile GPUs, and other available multicores processors, may be faster and much more efficient than their single threaded CPU counterparts. In this work, we present a novel approach for flocking boids simulation based on the Android renderscript API. We describe and implement a custom neighborhood grid, and present results with a simple game based on this platform.
Side Population in Human Non-Muscle Invasive Bladder Cancer Enriches for Cancer Stem Cells That Are Maintained by MAPK Signalling

Side population (SP) and ABC transporter expression enrich for stem cells in numerous tissues. We explored if this phenotype characterised human bladder cancer stem cells (CSCs) and attempted to identify regulatory mechanisms. Focusing on non-muscle invasive bladder cancer (NMIBC), multiple human cell lines were used to characterise SP and ABC transporter expression. In vitro and in vivo phenotypic and functional assessments of CSC behaviour were undertaken. Expression of putative CSC marker ABCG2 was assessed in clinical NMIBC samples (n = 148), and a role for MAPK signalling, a central mechanism of bladder tumourigenesis, was investigated. Results showed that the ABCG2 transporter was predominantly expressed and was up-regulated in the SP fraction by 3-fold (ABCG2hi) relative to the non-SP (NSP) fraction (ABCG2low). ABCG2hi SP cells displayed enrichment of stem cell markers (Nanog, Notch1 and SOX2) and a three-fold increase in colony forming efficiency (CFE) in comparison to ABCG2low NSP cells. In vivo, ABCG2hi SP cells enriched for tumour growth compared with ABCG2low NSP cells, consistent with CSCs. pERK was constitutively active in ABCG2hi SP cells and MEK inhibition also inhibited the ABCG2hi SP phenotype and significantly suppressed CFE. Furthermore, on examining clinical NMIBC samples, ABCG2 expression correlated with increased recurrence and decreased progression free survival. Additionally, pERK expression also correlated with decreased progression free survival, whilst a positive correlation was further demonstrated between ABCG2 and pERK expression. In conclusion, we confirm ABCG2hi SP enriches for CSCs in human NMIBC and MAPK/ERK pathway is a suitable therapeutic target.
Snapshot video: everyday photographers taking short video-clips

Camera phones and consumer digital cameras number hundreds of millions worldwide and most of them have the ability to take video in addition to photographs. Public discussions, marketing, and academic research often emphasize the new and innovative ways in which people use their ubiquitous digital cameras, especially camera phones, in combination with the Internet. In this paper we present our qualitative study of 13 people and their picture taking habits with regular cameras and camera phones. We focus on their videography practices in the context of their general use of photo and video media. Our results contradict the general assumption that the availability of ubiquitous video technology has significantly changed people's practices in home-mode pictorial communication. The models for capturing videos are often taken from situations in which previously taking snapshot photographs was the only option. Therefore, we suggest that mobile media creation and sharing technology has only gradually changed people's snapshot photography and videography practices.
Bacillus subtilis RecA with DprA–SsbA antagonizes RecX function during natural transformation

Abstract Bacillus subtilis DprA and RecX proteins, which interact with RecA, are crucial for efficient chromosomal and plasmid transformation. We showed that RecA, in the rATP·Mg2+ bound form (RecA·ATP), could not compete with RecX, SsbA or SsbB for assembly onto single-stranded (ss)DNA, but RecA·dATP partially displaced these proteins from ssDNA. RecX promoted reversible depolymerization of preformed RecA·ATP filaments. The two-component DprA–SsbA mediator reversed the RecX negative effect on RecA filament extension, but not DprA or DprA and SsbB. In the presence of DprA–SsbA, RecX added prior to RecA·ATP inhibited DNA strand exchange, but this inhibition was reversed when RecX was added after RecA. We propose that RecA nucleation is more sensitive to RecX action than is RecA filament growth. DprA–SsbA facilitates formation of an active RecA filament that directly antagonizes the inhibitory effects of RecX. RecX and DprA enable chromosomal transformation by altering RecA filament dynamics. DprA–SsbA and RecX proteins constitute a new regulatory network of RecA function. DprA–SsbA contributes to the formation of an active RecA filament and directly antagonizes the inhibitory effects of RecX during natural transformation.
Generating Referring Expressions Involving Relations

In this paper, we review Dale's [1989] algorithm for determining the content of a referring expression. The algorithm, which only permits the use of one-place predicates, it revised and extended to deal with n-ary predicates. We investigate the problem of blocking "recursion" in complex noun phrases and propose a solution in the context of our algorithm.
THE ABNORMALITIES OF THE INNER EAR IN KREISLER MICE.

The recessive gene kreisler (symbol kr ) was discovered by Hertwig (1942 a ), who later described its effects on behaviour (1942 b ) and the inner ear (1944, 1956). She found that it was possible to trace the anomalies of the ear back to 9-day embryos, when the otic vesicle can be seen to be situated in an abnormal position. The present study was aimed at discovering the cause of this abnormality, and at giving a fuller account of the later development of the ear. Material and Methods The particulars of the sectioned material are given in Table 1. Only litter-mate controls were used throughout. The embryos were fixed in Bouin9s fluid, sectioned at 7½ or 10 μ, depending on their age, and stained with Ehrlich9s haematoxylin and eosin. The older material was fixed in Witmaack9s fluid or formalin, sectioned at 10 μ, and stained either the same way or with cresyl violet or Weil9s iron haematoxylin.
The Effects of Alfvén Waves and Radiation Pressure in Dust Winds of Late-Type Stars

In the present study, we analyze the effects of a flux of Alfvén waves acting together with radiation pressure on grains as an acceleration mechanism of the wind of late-type stars. In the wind model, we simulate the presence of grains through a strong damping of the waves, and we use a nonisothermal profile for the temperature that is coherent with grain formation theories. We examine the changes in the velocity profile of the wind, and we show that if the grains are created in the region 1.1 < r/r0 < 2.0, their presence will affect the mass loss and terminal velocity. The model is applied to a K5 supergiant star and to Betelgeuse (α Ori).
The Complement Anaphylatoxin C5a Induces Apoptosis in Adrenomedullary Cells during Experimental Sepsis

Sepsis remains a poorly understood, enigmatic disease. One of the cascades crucially involved in its pathogenesis is the complement system. Especially the anaphylatoxin C5a has been shown to have numerous harmful effects during sepsis. We have investigated the impact of high levels of C5a on the adrenal medulla following cecal ligation and puncture (CLP)-induced sepsis in rats as well as the role of C5a on catecholamine production from pheochromocytoma-derived PC12 cells. There was significant apoptosis of adrenal medulla cells in rats 24 hrs after CLP, as assessed by the TUNEL technique. These effects could be reversed by dual-blockade of the C5a receptors, C5aR and C5L2. When rats were subjected to CLP, levels of C5a and norepinephrine were found to be antipodal as a function of time. PC12 cell production of norepinephrine and dopamine was significantly blunted following exposure to recombinant rat C5a in a time-dependent and dose-dependent manner. This impaired production could be related to C5a-induced initiation of apoptosis as defined by binding of Annexin V and Propidium Iodine to PC12 cells. Collectively, we describe a C5a-dependent induction of apoptotic events in cells of adrenal medulla in vivo and pheochromocytoma PC12 cells in vitro. These data suggest that experimental sepsis induces apoptosis of adrenomedullary cells, which are responsible for the bulk of endogenous catecholamines. Septic shock may be linked to these events. Since blockade of both C5a receptors virtually abolished adrenomedullary apoptosis in vivo, C5aR and C5L2 become promising targets with implications on future complement-blocking strategies in the clinical setting of sepsis.
mRNAs encoding the Aplysia homologues of fasciclin‐I and β‐thymosin are expressed only in the second phase of nerve injury and are differentially segregated in axons regenerating in vitro and in vivo

Studies using Aplysia californica have demonstrated that transcription after nerve injury occurs during a rapid, transient first phase and a delayed, prolonged second phase. Although the second phase is especially important for regeneration, the mRNAs produced during this phase have not been identified. We characterized two such mRNAs following axotomy. One encodes a novel fasciclin‐I homologue, Aplysia fasciclin‐like protein (apFasP), and the other encodes Aplysia β‐thymosin (apβT). In addition to mRNA synthesis, proteins required for regeneration must be available at the site of growth, and the transport and local translation of certain extrasomatic mRNAs aids in this process. We found apβT and apFasP proteins and mRNA at growth cones in vitro. However, only the mRNA for apβT was present in regenerating axons in vivo. This implies that the membrane protein apFasP is supplied by rapid transport from the soma, whereas the soluble apβT is synthesized locally. © 2005 Wiley‐Liss, Inc.
Do you remember what you did last summer? On the formation and alteration of memories for stressful experiences

A large body of evidence in animals and humans implicates the amygdala in promoting memory for arousing experiences. Although the amygdala can trigger threat-related noradrenergic-sympathetic arousal, in humans amygdala activation and noradrenergic-sympathetic arousal do not always concur. This raises the question how these two processes play a role in enhancing emotional declarative memory. The present study was designed to disentangle these processes in a combined subsequent-memory/fearconditioning paradigm with neutral items belonging to two conceptual categories as conditioned stimuli. Functional MRI, skin conductance (index of sympathetic activity), and pupil dilation (indirect index of central noradrenergic activity) were acquired throughout procedures. Recognition memory for individual items was tested 24h later. We found that pupil dilation and skin conductance responses were higher on CS+ (associated with a shock) compared to CStrials, irrespective of later memory for those items. By contrast, amygdala activity was only higher for CS+ items that were later confidently remembered compared to CS+ items that were later forgotten. Thus, amygdala activity and not noradrenergic-sympathetic arousal, predicted enhanced declarative item memory. This dissociation is in line with animal models stating that the amygdala integrates arousal-related neuromodulatory changes to alter mnemonic processes elsewhere in the brain. This chapter has been published as: de Voogd LD, Fernández G, Hermans EJ (2016) Disentangling the roles of arousal and amygdala activation in emotional declarative memory. Social Cognitive and Affective Neuroscience 11(9):1471–1480 (de Voogd et al., 2016b)
A Stacked Sub-Word Model for Joint Chinese Word Segmentation and Part-of-Speech Tagging

The large combined search space of joint word segmentation and Part-of-Speech (POS) tagging makes efficient decoding very hard. As a result, effective high order features representing rich contexts are inconvenient to use. In this work, we propose a novel stacked subword model for this task, concerning both efficiency and effectiveness. Our solution is a two step process. First, one word-based segmenter, one character-based segmenter and one local character classifier are trained to produce coarse segmentation and POS information. Second, the outputs of the three predictors are merged into sub-word sequences, which are further bracketed and labeled with POS tags by a fine-grained sub-word tagger. The coarse-to-fine search scheme is efficient, while in the sub-word tagging step rich contextual features can be approximately derived. Evaluation on the Penn Chinese Tree-bank shows that our model yields improvements over the best system reported in the literature.
Split Posterior Tibial Tendon Transfer for Varus Deformity of Hindfoot

Sixteen patients (23 feet) who underwent split posterior tibial tendon transfers were evaluated. The patients were seen on a followup basis for a minimum of 1 year postoperatively. The causes were spastic cerebral palsy in 13 feet, spastic-athetoid cerebral palsy in 3 feet, hydrocephalus in 3 feet, and other diseases in 4 feet. The indication for surgery was varus deformity during the stance phase of gait and increased varus deformity during the swing phase of gait because of spasticity of the posterior tibial muscle. Heel cord lengthening was done on 17 feet. Preoperative and postoperative gaits were evaluated while the patients were walking. Axial radiographs of the calcaneus and the tibia were taken of all patients while they were weightbearing. There were 15 excellent, 6 good, and 2 poor results. The poor ratings were assigned to patients who had recurrence of varus deformity; there were no cases of overcorrection. Split posterior tibial tendon transfer was effective for treating spastic varus deformity of the hind part of the foot. This treatment also could be considered for a patient with spastic-athetoid cerebral palsy, if the deformity was determined to be caused by overactivity of the tibialis posterior muscle.
Deciphering the molecular mechanism responsible for GCaMP6m's Ca2+-dependent change in fluorescence

The goal of this work is to determine how GCaMP6m’s fluorescence is altered in response to Ca2+-binding. Our detailed spectroscopic study reveals the simplest explanation for how GCaMP6m changes fluorescence in response to Ca2+ is with a four-state model, in which a Ca2+-dependent change of the chromophore protonation state, due to a shift in pKa, is the predominant factor. The pKa shift is quantitatively explained by a change in electrostatic potential around the chromophore due to the conformational changes that occur in the protein when calmodulin binds Ca2+ and interacts with the M13 peptide. The absolute pKa values for the Ca2+-free and Ca2+-saturated states of GCaMP6m are critical to its high signal-to-noise ratio. This mechanism has important implications for further improvements to GCaMP6m and potentially for other similarly designed biosensors.
Optimality of Poisson processes intensity learning with Gaussian processes

In this paper we provide theoretical support for the so-called "Sigmoidal Gaussian Cox Process" approach to learning the intensity of an inhomogeneous Poisson process on a d- dimensional domain. This method was proposed by Adams, Murray and MacKay (ICML, 2009), who developed a tractable computational approach and showed in simulation and real data experiments that it can work quite satisfactorily. The results presented in the present paper provide theoretical underpinning of the method. In particular, we show how to tune the priors on the hyper parameters of the model in order for the procedure to automatically adapt to the degree of smoothness of the unknown intensity, and to achieve optimal convergence rates.
Evolution of networks

We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrating the main features of evolving networks and discuss current approaches for their simulation and analytical study. Applications of the general results to particular networks in nature are discussed. We demonstrate the generic connections of the network growth processes with the general problems of non-equilibrium physics, econophysics, evolutionary biology, and so on.