Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Cornea Proteome: Identification and Quantitation of the Proteins of the Three Main Layers Including Epithelium, Stroma, and Endothelium

Diseases of the cornea are common and refer to conditions like infections, injuries and genetic defects. Morphologically, many corneal diseases affect only certain layers of the cornea and separate analysis of the individual layers is therefore of interest to explore the basic molecular mechanisms involved in corneal health and disease. In this study, the three main layers including, the epithelium, stroma and endothelium of healthy human corneas were isolated. Prior to analysis by LC–MS/MS the proteins from the different layers were either (i) separated by SDS-PAGE followed by in-gel trypsinization, (ii) in-solution digested without prior protein separation or, (iii) in-solution digested followed by cation exchange chromatography. A total of 3250 unique Swiss-Prot annotated proteins were identified in human corneas, 2737 in the epithelium, 1679 in the stroma, and 880 in the endothelial layer. Of these, 1787 proteins have not previously been identified in the human cornea by mass spectrometry. In total, 771 proteins were quantified, 157 based on in-solution digestion and 770 based on SDS-PAGE separation followed by in-gel digestion of excised gel pieces. Protein analysis showed that many of the identified proteins are plasma proteins involved in defense responses.
Improving Language Modeling using Densely Connected Recurrent Neural Networks

In this paper, we introduce the novel concept of densely connected layers into recurrent neural networks. We evaluate our proposed architecture on the Penn Treebank language modeling task. We show that we can obtain similar perplexity scores with six times fewer parameters compared to a standard stacked 2-layer LSTM model trained with dropout (Zaremba et al., 2014). In contrast with the current usage of skip connections, we show that densely connecting only a few stacked layers with skip connections already yields significant perplexity reductions.
Cell Type-Specific Separation of Subicular Principal Neurons during Network Activities

The hippocampal output structure, the subiculum, expresses two major memory relevant network rhythms, sharp wave ripple and gamma frequency oscillations. To this date, it remains unclear how the two distinct types of subicular principal cells, intrinsically bursting and regular spiking neurons, participate in these two network rhythms. Using concomitant local field potential and intracellular recordings in an in vitro mouse model that allows the investigation of both network rhythms, we found a cell type-specific segregation of principal neurons into participating intrinsically bursting and non-participating regular spiking cells. However, if regular spiking cells were kept at a more depolarized level, they did participate in a specific manner, suggesting a potential bimodal working model dependent on the level of excitation. Furthermore, intrinsically bursting and regular spiking cells exhibited divergent intrinsic membrane and synaptic properties in the active network. Thus, our results suggest a cell-type-specific segregation of principal cells into two separate groups during network activities, supporting the idea of two parallel streams of information processing within the subiculum.
A model for the design and evaluation of algorithms for closed-loop cardiovascular therapy

Developing a clinically useful closed-loop drug delivery system can be extremely time consuming and costly. One approach to reducing the time and cost associated with developing closed-loop systems is to reduce the number of animal experiments and perform an extensive set of simulation studies. Through simulations, a closed-loop controller's performance can be evaluated over a complete spectrum of the patient population, including boundary conditions. Simulation studies are repeatable, offering significant advantages in comparing modifications in control algorithms. Finally, simulation studies can be performed in a fraction of the time required for animal studies, at a fraction of the cost. We have developed a simulator, that included a nonlinear pulsatile-flow cardiovascular model, a physiological regulatory mechanism, and the pharmacology of four frequently titrated cardiovascular drugs. This simulator has already been used in the design and evaluation of two closed-loop algorithms-a self-tuning regulator (STR) and a multiple model adaptive controller (MMAC)-for blood pressure control during and after cardiac surgery.
Alteplase: descendancy in myocardial infarction, ascendancy in stroke

Tissue type plasminogen activator is available, through recombinant technology, for thrombolytic use as alteplase. Alteplase is relatively clot specific and should cause less bleeding side effects than the non-specific agents such as streptokinase. Alteplase has been used successfully in evolving myocardial infarction (MI) to reopen occluded coronary arteries. It is probably equally effective or superior to streptokinase in opening arteries and reducing mortality in MI. Alteplase is most effective when given early in MI and is probably ineffective when given 12 h after the onset of symptoms. The effectiveness of alteplase in MI can be increased by front loading with a bolus of 15 mg, followed by an infusion of 50 mg over 30 min and 35 mg over 60 min. Percutaneous transluminal coronary angioplasty or stenting is associated with a greater patency and lower rates of serious bleeding, recurrent ischaemia and death than alteplase in MI and is likely to take over from alteplase as the standard MI treatment. A reduced dose of alteplase to increase coronary artery patency prior to angioplasty may be useful in MI. An exciting new indication for the use of alteplase is in stroke, where it has become the first beneficial intervention. Alteplase is used to reopen occluded cerebral vessels but is associated with an increased risk of intracerebral haemorrhage. Alteplase is beneficial if given within 3 h of the onset of stroke but not after this time period. Therefore, the next challenge is to increase the percentage of people being diagnosed and treated within this period. Clinical trials have not established a role for alteplase in the treatment of acute coronary syndromes or deep vein thrombosis. However, alteplase is useful in treating pulmonary thromboembolism and peripheral vascular disease.
Mechanisms of two-color laser-induced field-free molecular orientation.

Two mechanisms of two-color (ω+2ω) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While the hyperpolarizability mechanism generates small amounts of orientation at intensities below the ionization threshold, ionization depletion quickly becomes the dominant mechanism as soon as ionizing intensities are reached. Only the ionization mechanism leads to substantial orientation (e.g., on the order of ≳0.1). For intensities typical of laser-induced molecular alignment and orientation experiments, the two mechanisms lead to robust, characteristic timings of the field-free orientation wave-packet revivals relative to the alignment revivals and the revival time. The revival timings can be used to detect the active orientation mechanism experimentally.
Characterizing Microblogs with Topic Models

As microblogging grows in popularity, services like Twitter are coming to support information gathering needs above and beyond their traditional roles as social networks. But most users’ interaction with Twitter is still primarily focused on their social graphs, forcing the often inappropriate conflation of “people I follow” with “stuff I want to read. ” We characterize some information needs that the current Twitter interface fails to support, and argue for better representations of content for solving these challenges. We present a scalable implementation of a partially supervised learning model (Labeled LDA) that maps the content of the Twitter feed into dimensions. These dimensions correspond roughly to substance, style, status, and social characteristics of posts. We characterize users and tweets using this model, and present results on two information consumption oriented tasks.
College Students' Usage of and Preferences for Print and Electronic Textbooks

Although print textbooks have been central for schooling for more than two centuries, electronic textbooks (e-textbooks) are steadily growing in popu-larity among students at all levels of education. This sharp growth has esca-lated the need for further research to enable a better understanding of the changing patterns of students’ usage of print and electronic media. The study explores college students’ usage of and preference for print and elec-tronic textbooks in Bahrain Teachers’ College, in Bahrain. The sample of the study consisted of 271 undergraduate students selected from courses that utilized both formats of textbook as clearly indicated in their syllabi. De-scriptive analyses were used to analyze data collected. Results indicate that regardless of textbook format, the highest percentage of students use their textbooks only when their instructors require them to do so. For print text-books, results show that the highest percentage of students spend between 1 to 3 hours a week on reading. However, for e-textbooks, the highest per-centage of students spend only less than 1 hour per week on reading. An in-teresting finding for this study is that compared to print textbooks, e-textbooks gain a higher percentage of students’ usage when it comes to spending higher numbers of hours of reading per week. The study affirms that students are in general positive to the use of electronic format but still show a preference for print format as the best medium for academic study. Lastly, the study uncovers reasonable findings as to why students prefer one textbook format over the other.
Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability

Viral integration into the human genome upon infection is an important risk factor for various human malignancies. We developed viral integration site detection tool called Virus-Clip, which makes use of information extracted from soft-clipped sequencing reads to identify exact positions of human and virus breakpoints of integration events. With initial read alignment to virus reference genome and streamlined procedures, Virus-Clip delivers a simple, fast and memory-efficient solution to viral integration site detection. Moreover, it can also automatically annotate the integration events with the corresponding affected human genes. Virus-Clip has been verified using whole-transcriptome sequencing data and its detection was validated to have satisfactory sensitivity and specificity. Marked advancement in performance was detected, compared to existing tools. It is applicable to versatile types of data including whole-genome sequencing, whole-transcriptome sequencing, and targeted sequencing. Virus-Clip is available at http://web.hku. hk/~dwhho/Virus-Clip.zip.
A Compact Model for Single Event Effects in PD SOI Sub-Micron MOSFETs

This paper presents a compact model implemented in Verilog-A for partially depleted (PD) silicon-on-insulator (SOI) sub-micron MOSFETs, which allows for describing the Single Events Effects (SEE) produced by heavy ions. This Verilog-A module can be coupled with Spice simulator in order to have faster (time-efficient) circuit simulations with good agreement. Due to the physical aspects considered in the model, better flexibility than the standard current source method is achieved. Experimental data for 0.15 and <formula formulatype="inline"> <tex Notation="TeX">${0.13}~\mu{\rm m}$</tex></formula> technology nodes are used to validate our model. Robustness of the model to reproduce experimental results is demonstrated on three data-sets available in literature: 1) single event transient current in stand-alone n-FET from <formula formulatype="inline"> <tex Notation="TeX">${0.13}~\mu{\rm m}$</tex></formula> PD SOI process hinted by heavy ions at different positions; 2) SEE propagation in path delay with ten inverters realized in <formula formulatype="inline"><tex Notation="TeX">${0.13}~\mu{\rm m}$</tex></formula> PD SOI process; 3) 6T SRAMs with active element delay on SEE-rad-hardened <formula formulatype="inline"><tex Notation="TeX">$0.15~\mu{\rm m}$</tex></formula> PD SOI process.
Induction of Bcl‐3 by acute binge alcohol results in Toll‐like receptor 4/LPS tolerance

Acute alcohol binge results in immunosuppression and impaired production of proinflammatory cytokines, including TNF‐α. TNF‐α production is induced by LPS, a TLR4 ligand, and is tightly regulated at various levels of the signaling cascade, including the NF‐κB transcription factor. Here, we hypothesized that acute alcohol induces TLR4/LPS tolerance via Bcl‐3, a nuclear protein and member of the NF‐κB family. We found that acute alcohol pretreatment resulted in the same attenuating effect as LPS pretreatment on TLR4‐induced TNF‐α production in human monocytes and murine RAW 264.7 macrophages. Acute alcohol‐induced Bcl‐3 expression and IP studies revealed increased association of Bcl‐3 with NF‐κB p50 homodimers in alcohol‐treated macrophages and in mice. ChIP assays revealed increased occupancy of Bcl‐3 and p50 at the promoter region of TNF‐α in alcohol‐pretreated cells. To confirm that the Bcl‐3–p50 complex regulates transcription/production of TNF‐α during acute alcohol exposure, we inhibited Bcl‐3 expression using a targeted siRNA. Bcl‐3 knockdown prevented the alcohol‐induced inhibition of TNF‐α mRNA and protein production. In a mouse model of binge alcohol, an increase in Bcl‐3 and a concomitant decrease in TNF‐α but no change in IL‐10 production were found in mice that received alcohol followed by LPS challenge. In summary, our novel data suggest that acute alcohol treatment in vitro and in vivo induces molecular signatures of TLR4/LPS tolerance through the induction of Bcl‐3, a negative regulator of TNF‐α transcription via its association with NF‐κB p50/p50 dimers.
Path Feasibility Analysis of BPEL Processes under Dead Path Elimination Semantics

SUMMARY Web Service Business Process Execution Language (BPEL) has become the de facto standard for developing instant service-oriented workﬂow applications in open environment. The correctness and reliability of BPEL processes have gained increasing concerns. However, the unique features (e.g., dead path elimination (DPE) semantics, parallelism, etc.) of BPEL language have raised enormous problems to it, especially in path feasibility analysis of BPEL processes. Path feasibility analysis of BPEL processes is the basis of BPEL testing, for it relates to the test case generation. Since BPEL processes support both parallelism and DPE semantics, existing techniques can’t be directly applied to its path feasibility analysis. To address this problem, we present a novel technique to analyze the path feasibility for BPEL processes. First, to tackle unique features mentioned above, we transform a BPEL process into an intermediary model — BPEL control ﬂow graph, which is proposed to abstract the execution ﬂow of BPEL processes. Second, based on this abstraction, we symbolically encode every path of BPEL processes as some Satisﬁability formulas. Finally, we solve these formulas with the help of Satisﬁability Modulo Theory (SMT) solvers and the feasible paths of BPEL processes are obtained. We illustrate the applicability and feasibility of our technique through a case study.
Competing Cues: Older Adults Rely on Knowledge in the Face of Fluency

Consumers regularly encounter repeated false claims in political and marketing campaigns, but very little empirical work addresses their impact among older adults. Repeated statements feel easier to process, and thus more truthful, than new ones (i.e., illusory truth). When judging truth, older adults’ accumulated general knowledge may offset this perception of fluency. In two experiments, participants read statements that contradicted information stored in memory; a post-experimental knowledge check confirmed what individual participants knew. Unlike young adults, older adults exhibited illusory truth only when they lacked knowledge about claims. This interaction between knowledge and fluency extends dual-process theories of aging.
The UKIRT wide field camera ZYJHK photometric system: calibration from 2MASS

In this paper, we describe the photometric calibration of data taken with the near-infrared Wide Field Camera (WFCAM) on the United Kingdom Infrared Telescope (UKIRT). The broad-band ZYJHK data are directly calibrated from Two-Micron All-Sky Survey (2MASS) point sources which are abundant in every WFCAM pointing. We perform an analysis of spatial systematics in the photometric calibration, both inter- and intradetector show that these are present at up to the ∼5 per cent level in WFCAM. Although the causes of these systematics are not yet fully understood, a method for their removal is developed and tested. Following the application of the correction procedure, the photometric calibration of WFCAM is found to be accurate to ≃1.5 per cent for the JHK bands and 2 per cent for the ZY bands, meeting the survey requirements. We investigate the transformations between the 2MASS and WFCAM systems and find that the Z and Y calibrations are sensitive to the effects of interstellar reddening for large values of E(B - V)', but that the JHK filters remain largely unaffected. We measure a small correction to the WFCAM Y-band photometry required to place WFCAM on a Vega system, and investigate WFCAM measurements of published standard stars from the list of UKIRT faint standards. Finally, we present empirically determined throughput measurements for WFCAM.
A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study

Genetic variants in intron 1 of the fat mass– and obesity-associated (FTO) gene have been consistently associated with body mass index (BMI) in Europeans. However, follow-up studies in African Americans (AA) have shown no support for some of the most consistently BMI–associated FTO index single nucleotide polymorphisms (SNPs). This is most likely explained by different race-specific linkage disequilibrium (LD) patterns and lower correlation overall in AA, which provides the opportunity to fine-map this region and narrow in on the functional variant. To comprehensively explore the 16q12.2/FTO locus and to search for second independent signals in the broader region, we fine-mapped a 646–kb region, encompassing the large FTO gene and the flanking gene RPGRIP1L by investigating a total of 3,756 variants (1,529 genotyped and 2,227 imputed variants) in 20,488 AAs across five studies. We observed associations between BMI and variants in the known FTO intron 1 locus: the SNP with the most significant p-value, rs56137030 (8.3×10−6) had not been highlighted in previous studies. While rs56137030was correlated at r2>0.5 with 103 SNPs in Europeans (including the GWAS index SNPs), this number was reduced to 28 SNPs in AA. Among rs56137030 and the 28 correlated SNPs, six were located within candidate intronic regulatory elements, including rs1421085, for which we predicted allele-specific binding affinity for the transcription factor CUX1, which has recently been implicated in the regulation of FTO. We did not find strong evidence for a second independent signal in the broader region. In summary, this large fine-mapping study in AA has substantially reduced the number of common alleles that are likely to be functional candidates of the known FTO locus. Importantly our study demonstrated that comprehensive fine-mapping in AA provides a powerful approach to narrow in on the functional candidate(s) underlying the initial GWAS findings in European populations.
Prevention of esophagopharyngeal reflux by augmenting the upper esophageal sphincter pressure barrier

Incompetence of the upper esophageal sphincter (UES) is fundamental to the occurrence of esophagopharyngeal reflux (EPR), and development of supraesophageal manifestations of reflux disease (SERD). However, therapeutic approaches to SERD have not been directed to strengthening of the UES barrier function. Our aims were to demonstrate that EPR events can be experimentally induced in SERD patients and not in healthy controls, and ascertain if these events can be prevented by application of a modest external cricoid pressure.
Mechanism of Phosphorylation-induced Activation of Phospholipase C-γ Isozymes*♦

The lipase activity of most phospholipases C (PLCs) is basally repressed by a highly degenerate and mostly disordered X/Y linker inserted within the catalytic domain. Release of this auto-inhibition is driven by electrostatic repulsion between the plasma membrane and the electronegative X/Y linker. In contrast, PLC-γ isozymes (PLC-γ1 and -γ2) are structurally distinct from other PLCs because multiple domains are present in their X/Y linker. Moreover, although many tyrosine kinases directly phosphorylate PLC-γ isozymes to enhance their lipase activity, the underlying molecular mechanism of this activation remains unclear. Here we define the mechanism for the unique regulation of PLC-γ isozymes by their X/Y linker. Specifically, we identify the C-terminal SH2 domain within the X/Y linker as the critical determinant for auto-inhibition. Tyrosine phosphorylation of the X/Y linker mediates high affinity intramolecular interaction with the C-terminal SH2 domain that is coupled to a large conformational rearrangement and release of auto-inhibition. Consequently, PLC-γ isozymes link phosphorylation to phospholipase activation by elaborating upon primordial regulatory mechanisms found in other PLCs.
Generalized Belief Operator and the Impact of Small Probability Events on Higher Order Beliefs

This paper studies the robustness of an equilibrium to incomplete information in binary-action supermodular games. Using a generalized version of belief operator, we explore the restrictions that prior beliefs impose on higher order beliefs. In particular, we obtain a non-trivial lower bound on the probability of a common belief event, uniform over type spaces, when the underlying game has a monotone potential. Conversely, when the game has no monotone potential, we construct a type space with an arbitrarily high probability event in which players never have common belief about that event. As an implication of these results, we show for generic binary-action supermodular games that an action profile is robust to incomplete information if and only if it is a monotone potential maximizer. Our study offers new methodology and insight to the analysis of global game equilibrium selection.
A comparison of asynchronous QDI templates using static logic

Asynchronous quasi-delay-insensitive (QDI) circuits are a promising solution for coping with aggressive process variations faced by modern technologies, as they can gracefully accommodate gate and wire delay variations. The literature proposes several QDI design templates with different trade-offs, giving designers a large spectrum of options to use, adapt or even mix. Among these, NULL Convention Logic (NCL), NCL+, Autonomous Signal-Validity Half-Buffer (ASVHB) and Sleep Convention Logic (SCL) are potential alternatives for low and ultra-low power applications. This paper evaluates these four QDI templates through an 8-bit Kogge-Stone full adder case study, showing analysis on cycle time, energy per operation, leakage power, energy-delay product (EDP), leakage-delay product (LDP) and area consumption. It also qualitatively evaluates each template, pointing out specific characteristics that can be suitable for low power applications.