Miracle-dz/UniFAR-FTUs huggingface dataset:
Selected Published Abstracts of Baylor Researchers

Results: Hepatocellular carcinoma was detected before liver transplant in 78% and discovered incidentally in 22%. The cause of cirrhosis was hepatitis C (HCV) (55%), hepatitis B (HBV) (17%), alcohol (9%), and other/unknown (19%). Although AFP was elevated 62%, the median level was 15 ng/mL. Only 26%, 15% and 13% were more than 100, 400 and 1000 ng/mL, respectively. By comparison, AFP was elevated in 20% without HCC, but exceeded 100 ng/mL in only 3%. The overall accuracy of AFP was poor regardless of the cutoff. Magnetic resonance imaging was more accurate than computerized tomography or ultrasound in detecting tumour, particularly when performed within 3 months of transplant.
Weighted Least Squares Estimates of Return Predictability Regressions

Time varying volatility causes substantial heteroskedasticity in return predictability regressions, making OLS estimates less efficient than least squares estimates weighted by ex-ante return variance (WLS-EV). In small sample simulations, I show that using WLS-EV instead of OLS results in large efficiency gains, fewer false negatives, and avoids the bias associated with ex-post weighting schemes. Using WLS-EV also changes several important conclusions based on OLS estimates: traditional predictors such as the dividend-to-price ratio perform better in- and out-of-sample, whereas WLS-EV estimates of the predictability afforded by proxies for the variance risk premium, politics, the weather, and the stars are not significant.
Administering GBrowse Sites with WebGBrowse

GBrowse is widely used by biologists to visualize genome annotation. We have developed WebGBrowse to facilitate hosting multiple GBrowse instances specific for different users on the same Web server. WebGBrowse automatically sets up each user‐specific GBrowse instance by extracting information from user‐supplied data to produce the appropriate configuration. This unit describes installation and administration of WebGBrowse for bioinformaticians who plan to manage local WebGBrowse servers in their institutions.Curr. Protoc. Bioinform. 33:9.14. 1‐9.14. 9. © 2011 by John Wiley & Sons, Inc.
Chronic Glucocorticoid Deficiency‐Induced Abnormal Aggression, Autonomic Hypoarousal, and Social Deficit in Rats

Certain aggression‐related psychopathologies are associated with decreased glucocorticoid production and autonomic functions in humans. We have previously shown that experimentally‐induced chronic glucocorticoid deficiency leads to abnormal forms of attack in rats. Here, we compared the effects of acute and chronic glucocorticoid deficiency on aggressive behaviour, autonomic responses to challenges, and anxiety. Glucocorticoid synthesis was blocked acutely by the glucocorticoid synthesis blocker metyrapone or chronically by adrenalectomy and low glucocorticoid replacement (ADXr). As shown previously, chronic glucocorticoid deficiency facilitated aberrant attacks directed towards the most vulnerable parts of the opponent's body. The acute inhibition of glucocorticoid synthesis lowered aggressive behaviour without affecting attack targeting. In a different experiment, ADXr rats and their sham‐operated controls were exposed to different challenges whereas their heart rate and locomotion were telemetrically recorded. Autonomic responses to social challenges were lowered by chronic, but not by acute glucocorticoid deficiency. Autonomic responses to the elevated plus‐maze were only slightly affected by chronic glucocorticoid deficiency. Locomotor behaviour was not affected in either challenge; thus, the altered autonomic reactions were not due to interference from workload. The behaviour of ADXr rats was similar to that of sham‐operated controls in the elevated plus‐maze, but ADXr rats showed reduced social interactions in the social interaction test. Our data demonstrate that, in rats, chronic but not acute glucocorticoid deficiency induces abnormal attack patterns, deviant cardiovascular responses and social deficits that are similar to those seen in abnormally violent humans. Thus, the similar correlations found in humans probably cover a causal relationship. Experimentally‐induced glucocorticoid deficiency may be used to assess the mechanisms underlying glucocorticoid deficiency‐induced abnormal forms of aggressiveness.
Transcriptional Upregulation of Cav3.2 Mediates Epileptogenesis in the Pilocarpine Model of Epilepsy

In both humans and animals, an insult to the brain can lead, after a variable latent period, to the appearance of spontaneous epileptic seizures that persist for life. The underlying processes, collectively referred to as epileptogenesis, include multiple structural and functional neuronal alterations. We have identified the T-type Ca2+ channel Cav3.2 as a central player in epileptogenesis. We show that a transient and selective upregulation of Cav3.2 subunits on the mRNA and protein levels after status epilepticus causes an increase in cellular T-type Ca2+ currents and a transitional increase in intrinsic burst firing. These functional changes are absent in mice lacking Cav3.2 subunits. Intriguingly, the development of neuropathological hallmarks of chronic epilepsy, such as subfield-specific neuron loss in the hippocampal formation and mossy fiber sprouting, was virtually completely absent in Cav3.2−/− mice. In addition, the appearance of spontaneous seizures was dramatically reduced in these mice. Together, these data establish transcriptional induction of Cav3.2 as a critical step in epileptogenesis and neuronal vulnerability.
Structure and function of bacterial outer membrane proteins: barrels in a nutshell

The outer membrane protects Gram‐negative bacteria against a harsh environment. At the same time, the embedded proteins fulfil a number of tasks that are crucial to the bacterial cell, such as solute and protein translocation, as well as signal transduction. Unlike membrane proteins from all other sources, integral outer membrane proteins do not consist of transmembrane α‐helices, but instead fold into antiparallel β‐barrels. Over recent years, the atomic structures of several outer membrane proteins, belonging to six families, have been determined. They include the OmpA membrane domain, the OmpX protein, phospholipase A, general porins (OmpF, PhoE), substrate‐specific porins (LamB, ScrY) and the TonB‐dependent iron siderophore transporters FhuA and FepA. These crystallographic studies have yielded invaluable insight into and decisively advanced the understanding of the functions of these intriguing proteins. Our review is aimed at discussing their common principles and peculiarities as well as open questions associated with them.
Thermally Stable Solution Processed Vanadium Oxide as a Hole Extraction Layer in Organic Solar Cells

Low-temperature solution-processable vanadium oxide (V2Ox) thin films have been employed as hole extraction layers (HELs) in polymer bulk heterojunction solar cells. V2Ox films were fabricated in air by spin-coating vanadium(V) oxytriisopropoxide (s-V2Ox) at room temperature without the need for further thermal annealing. The deposited vanadium(V) oxytriisopropoxide film undergoes hydrolysis in air, converting to V2Ox with optical and electronic properties comparable to vacuum-deposited V2O5. When s-V2Ox thin films were annealed in air at temperatures of 100 °C and 200 °C, OPV devices showed similar results with good thermal stability and better light transparency. Annealing at 300 °C and 400 °C resulted in a power conversion efficiency (PCE) of 5% with a decrement approximately 15% lower than that of unannealed films; this is due to the relative decrease in the shunt resistance (Rsh) and an increase in the series resistance (Rs) related to changes in the oxidation state of vanadium.
Single-Anchor Two-Way Localization Bounds for 5G mmWave Systems

Recently, millimeter-wave (mmWave) 5G localization has been shown to be to provide centimeter-level accuracy, lending itself to many location-aware applications, e.g., connected autonomous vehicles (CAVs). One assumption usually made in the investigation of localization methods is that the user equipment (UE), i.e., a CAV, and the base station (BS) are time synchronized. In this paper, we remove this assumption and investigate two two-way localization protocols: (i) a round-trip localization protocol (RLP), whereby the BS and UE exchange signals in two rounds of transmission and then localization is achieved using the signal received in the second round; (ii) a collaborative localization protocol (CLP), whereby localization is achieved using the signals received in the two rounds. We derive the position and orientation error bounds applying beamforming at both ends and compare them to the traditional one-way localization. Our results show that mmWave localization is mainly limited by the angular rather than the temporal estimation and that CLP significantly outperforms RLP. Our simulations also show that it is more beneficial to have more antennas at the BS than at the UE.
Extraction of Code-mixed Aspect Topics in Semantic Representation

With recent advancements and popularity of social networking forums, millions of people virtually connected to the World Wide Web, commonly communicate in multiple languages. This has led to the generation of large volumes of unstructured code-mixed social media text having useful aspects of information highly dispersed. Aspect based opinion mining relates opinion targets to their polarity values, in a specific context. It is known that since aspects are often implicit, detecting and retrieving them is a difficult task. Moreover, it is very challenging as the code-mixed social media text suffers from its associated linguistic complexities. As a standard, topic modeling has a potential of extracting aspects pertaining to opinion data from large text. This results not only in retrieval of implicit aspects but also in clustering them together. In this paper we propose knowledge based language independent code-mixed semantic LDA (lcms-LDA) model, with an aim to improve the coherence of clusters. We find that the proposed lcms-LDA model infers topic distributions without language barrier, based on semantics associated with words. Our experimental results showed an increase in the UMass and KL divergence score indicating an improved performance in the resulting coherence and distinctiveness of aspect clusters in comparison with the state-of-the-art techniques used for aspect extraction of code-mixed data.
High‐field MRS of the human brain at short TE and TR

In vivo MRS of the human brain at 7 tesla allows identification of a large number of metabolites at higher spatial resolutions than currently possible at lower field strengths. However, several challenges complicate in vivo localization and artifact suppression in MRS at high spatial resolution within a clinically feasible scan time at 7 tesla. Published MRS sequences at 7 tesla suffer from long echo times, inherent signal‐to‐noise ratio (SNR) loss, large chemical shift displacement artifacts or long repetition times because of excessive radiofrequency (RF) power deposition. In the present study a pulse‐acquire sequence was used that does not suffer from these high field drawbacks. A slice selective excitation combined with high resolution chemical shift imaging for in‐plane localization was used to limit chemical shift displacement artifacts. The pulse‐acquire approach resulted in a very short echo time of 1.4 ms. A cost function guided shimming algorithm was developed to constrain frequency offsets in the excited slice, therefore adiabatic frequency selective suppression could be employed to minimize artifacts from high intensity lipids and water signals in the excited slice. The high sensitivity at a TR of 1 s was demonstrated both on a supraventricular slice as well as in an area very close to the skull in the frontal cortex at a nominal spatial resolution of 0.25 cc within a feasible scan time. Copyright © 2011 John Wiley & Sons, Ltd.
How Much Labor Do You Need to Manage Capital?

Asset management companies in the United States employ several hundred thousand people in advisory, portfolio management, and research roles, yet academic research suggests their investments, on average, underperform passive benchmarks net of fees. Using a new dataset on over 10,000 registered investment advisors (RIAs), we analyze which clienteles, asset classes, and strategies require more human capital, as well as the value that human capital adds to investment management. We find that while more human capital is not associated with better performance (controlling for assets under management), having more advisory personnel helps attract more assets, justifying their salaries from the point of view of the firm. Furthermore, larger teams actually behave more like closet-indexers, holding more diversified portfolios with lower tracking error. Our findings suggest that some active management companies realize their ability, or lack thereof, to generate alpha, and use their employees in order to keep and attract clients.
Polymers of Intrinsic Microporosity

This paper focuses on polymers that demonstrate microporosity without possessing a network of covalent bonds—the so-called polymers of intrinsic microporosity (PIM). PIMs combine solution processability and microporosity with structural diversity and have proven utility for making membranes and sensors. After a historical account of the development of PIMs, their synthesis is described along with a comprehensive review of the PIMs that have been prepared to date. The important methods of characterising intrinsic microporosity, such as gas absorption, are outlined and structure-property relationships explained. Finally, the applications of PIMs as sensors and membranes for gas and vapour separations, organic nanofiltration, and pervaporation are described.
Introducing LIVA to Measure Long-Term Firm Performance

In this paper we introduce lifetime (or long-term) investor value appropriation (LIVA) to measure firm performance, defined as the ex post value of discounted cash flows over a firm’s lifetime (or several decades). Unlike other commonly used measures of firm performance, such as return on assets, Tobin’s q, economic profit, or total shareholder return, LIVA captures long-term returns vis- a-vis the cost of capital, profitable growth, as well as the size of the economic impact in a single metric. Moreover, we show that LIVA can be equivalently operationalized using cash flow data, accounting profits, or shareholder return data. Finally, two exploratory empirical studies illustrate how LIVA can be operationalized and provide new strategic insights beyond currently used measures.
The histone methyltransferase SETD2 is required for expression of acrosin-binding protein 1 and protamines and essential for spermiogenesis in mice

Spermatogenesis is precisely controlled by complex gene expression programs and involves epigenetic reprogramming, including histone modification and DNA methylation. SET domain–containing 2 (SETD2) is the predominant histone methyltransferase catalyzing the trimethylation of histone H3 lysine 36 (H3K36me3) and plays key roles in embryonic stem cell differentiation and somatic cell development. However, its role in male germ cell development remains elusive. Here, we demonstrate an essential role of Setd2 for spermiogenesis, the final stage of spermatogenesis. Using RNA-seq, we found that, in postnatal mouse testes, Setd2 mRNA levels dramatically increase in 14-day-old mice. Using a germ cell–specific Setd2 knockout mouse model, we also found that targeted Setd2 knockout in germ cells causes aberrant spermiogenesis with acrosomal malformation before step 8 of the round-spermatid stage, resulting in complete infertility. Furthermore, we noted that the Setd2 deficiency results in complete loss of H3K36me3 and significantly decreases expression of thousands of genes, including those encoding acrosin-binding protein 1 (Acrbp1) and protamines, required for spermatogenesis. Our findings thus reveal a previously unappreciated role of the SETD2-dependent H3K36me3 modification in spermiogenesis and provide clues to the molecular mechanisms in epigenetic disorders underlying male infertility.
Reactive Oxygen Species, Superoxide Dimutases, and PTEN-p53-AKT-MDM2 Signaling Loop Network in Mesenchymal Stem/Stromal Cells Regulation

Mesenchymal stromal/stem cells (MSCs) are multipotent cells that can differentiate to various specialized cells, which have the potential capacity to differentiate properly and accelerate recovery in damaged sites of the body. This stem cell technology has become the fundamental element in regenerative medicine. As reactive oxygen species (ROS) have been reported to adversely influence stem cell properties, it is imperative to attenuate the extent of ROS to the promising protective approach with MSCs’ regenerative therapy. Oxidative stress also affects the culture expansion and longevity of MSCs. Therefore, there is great need to identify a method to prevent oxidative stress and replicative senescence in MSCs. Phosphatase and tensin homologue deleted on chromosome 10/Protein kinase B, PKB (PTEN/AKT) and the tumor suppressor p53 pathway have been proven to play a pivotal role in regulating cell apoptosis by regulating the oxidative stress and/or ROS quenching. In this review, we summarize the current research and our view of how PTEN/AKT and p53 with their partners transduce signals downstream, and what the implications are for MSCs’ biology.
Regional Variations in the Transport of Interleukin-1α across the Blood-Brain Barrier in ICR and Aging SAMP8 Mice

Objectives: The blood-brain barrier (BBB) transports blood-borne interleukin-1α (IL-1) into the brain by a saturable process. Here, we determined whether all regions of the brain could transport IL-1 and whether transport differed between ICR and SAMP8 mice, a strain which overexpresses amyloid beta protein (Aβ) with aging. Methods: We used multiple-time regression analysis to measure the unidirectional influx rate (transport rate) of radioactively labeled IL-1 for 10 brain regions in young (2 months old) ICR mice and in young and aged (17 months old) SAMP8 mice. We also used radioactively labeled sucrose and albumin to determine whether the BBB was disrupted in aged SAMP8 mice. Results: In young ICR mice, eight of the 10 brain regions transported IL-1, with the pons-medulla having the fastest transport rate (0.584 ± 0.163 µl/g·min), but no statistically significant differences occurred among regions. In SAMP8 mice, only four regions transported IL-1. In young SAMP8 mice, the pons-medulla transported IL-1 faster than any other region (0.642 ± 0.197 µl/g·min), a rate that was significantly different (p < 0.01) from each of the other regions. Aged SAMP8 mice had a similar regional transport pattern to young SAMP8 mice, but there were no statistically significant differences among the four transporting regions. Sucrose and albumin spaces were not increased in aged SAMP8 mice, demonstrating an intact BBB. Conclusions: The smaller number of regions transporting IL-1 in SAMP8 mice as compared to ICR mice demonstrates a genetic influence on transport which could alter the ability of blood-borne IL-1 to directly affect brain functions. No evidence of BBB disruption was found in the aged SAMP8 mice from this colony.
Uniformly embedded silver nanomesh as highly bendable transparent conducting electrode

Ag-nanomesh-based highly bendable conducting electrodes are developed using a combination of metal nanotransfer printing and embossing for the 6-inch wafer scale. Two Ag nanomeshes, including pitch sizes of 7.5 and 10 μm, are used to obtain highly transparent (approximately 85% transmittance at a wavelength of 550 nm) and electrically conducting properties (below 10 Ω sq−1). The Ag nanomeshes are also distinguished according to the fabrication process, which is called transferred or embedded Ag nanomesh on polyethylene terephthalate (PET) substrate, in order to compare their stability against bending stress. Then the enhancement of bending stability when the Ag nanomesh is embedded in the PET substrate is confirmed.
Identification, Bioinformatics Analyses, and Expression of Immunoreactive Antigens of Mycoplasma haemofelis

ABSTRACT Mycoplasma haemofelis infection frequently causes anemia in cats. Despite an intense immune response and/or antibiotic treatment, cats often remain asymptomatic carriers following infection. Our hypothesis is that detection of antibodies to M. haemofelis is a sensitive approach for identifying infected cats, particularly carriers. To date, no immunoassay has been developed. This is due largely to the inability to culture M. haemofelis in vitro; hence, a source of antigen is not readily available. The objective of this study was to identify, express, and purify immunogenic proteins of M. haemofelis. To accomplish this, two whole-genomic expression libraries were created in the Lambda ZapII vector and immunoscreened with preimmune plasma, plasma from specific-pathogen-free cats, and pooled acute- and convalescent-phase plasma from experimentally infected cats. The inserts from 21 immunoreactive clones were sequenced, resulting in the identification of 60 genes coding for putative proteins necessary for diverse cellular functions, along with several novel genes of M. haemofelis. Fragments of selected genes based on bioinformatic analyses were PCR amplified, cloned into a high-level protein expression system, and subsequently expressed in Escherichia coli as a His6-fusion protein. The recombinant fusion proteins of M. haemofelis were purified and evaluated as an antigen in a Western blot to verify the findings of previous immunoscreening. Together with bioinformatics analyses of individual genes, this approach provided several putative candidate antigens. Five antigens of M. haemofelis were reactive by Western blotting against the immune plasma and negative against nonimmune plasma; these antigens might be useful serologic or even vaccine targets.
Factors Influence Internal Audit Effectiveness

This study aims to examine to what extent internal audit effectiveness could be influenced by selected factors namely internal audit scope, internal auditor’s experience and senior management's response in the Omani public sector. Employing questionnaire including four sections with 48 questions for responds of 45 managers and 163 employees in Public Authority for Social Insurance (PASI) in the Sultanate of Oman, descriptive analysis, correlation analysis, and multiple regressions were employed to examine the relationships among the study’s variables. The study found that a significant relationship between internal audit effectiveness and its scope and auditors’ experience in the employees’ sample while they were insignificant in the managers’ sample. Finally, it is found that there is insignificant relationship between internal audit effectiveness and senior management's response. Based on the findings, an awareness has to be maximized on employees to better cooperate with internal audit staff to improve the applications of internal audit standards. Managers are well interested in organization’s activities and performance depending on the internal audit findings and observations. The board of directors has to take in its considerations the reasons of these insignificant results if the reasons are not related to the small size of the managers’ sample. The study’s contribution is to provide evidence regarding the influence of three mentioned factors on the internal audit effectiveness in public sector.