Triple Helix, Fall 2018

Table of Contents: Science Agenda: The Politics of Grant Writing / by Kavya Rajesh (p. 4) -- From the Experts / by Katherine Bruner (p. 5) -- 3D Printed Drugs: The Future of Pharmaceuticals / by Ethan Wang (p. 6) -- Computerized Markets: Wall Street Takeover / by James Kiraly (p. 10) -- The Evolution of Fear / by Alisha Ahmed (p. 14) -- ADDing Up / by Victor Liaw (p. 18) -- The Clone Wars / by Jina Zhou (p. 22) -- Physician-Assisted Suicide: Drawing the Line / by Haley Wolf (p. 26) -- Supervised Injection Sites / by Alex Gajewski (p. 30) -- On Emerging Medicalization and Health Care / by Patrick Lee (p. 33) -- The Future of Human Gene Modifications / by Elizabeth Robinson (p. 36)College of Natural SciencesUT LibrariesLiberal Art

People's Perceptions Toward Bias and Related Concepts in Large Language Models: A Systematic Review

Large language models (LLMs) have brought breakthroughs in tasks including translation, summarization, information retrieval, and language generation, gaining growing interest in the CHI community. Meanwhile, the literature shows researchers' controversial perceptions about the efficacy, ethics, and intellectual abilities of LLMs. However, we do not know how lay people perceive LLMs that are pervasive in everyday tools, specifically regarding their experience with LLMs around bias, stereotypes, social norms, or safety. In this study, we conducted a systematic review to understand what empirical insights papers have gathered about people's perceptions toward LLMs. From a total of 231 retrieved papers, we full-text reviewed 15 papers that recruited human evaluators to assess their experiences with LLMs. We report different biases and related concepts investigated by these studies, four broader LLM application areas, the evaluators' perceptions toward LLMs' performances including advantages, biases, and conflicting perceptions, factors influencing these perceptions, and concerns about LLM applications

Methylcap-Seq Reveals Novel DNA Methylation Markers for the Diagnosis and Recurrence Prediction of Bladder Cancer in a Chinese Population

PURPOSE: There is a need to supplement or supplant the conventional diagnostic tools, namely, cystoscopy and B-type ultrasound, for bladder cancer (BC). We aimed to identify novel DNA methylation markers for BC through genome-wide profiling of BC cell lines and subsequent methylation-specific PCR (MSP) screening of clinical urine samples. EXPERIMENTAL DESIGN: The methyl-DNA binding domain (MBD) capture technique, methylCap/seq, was performed to screen for specific hypermethylated CpG islands in two BC cell lines (5637 and T24). The top one hundred hypermethylated targets were sequentially screened by MSP in urine samples to gradually narrow the target number and optimize the composition of the diagnostic panel. The diagnostic performance of the obtained panel was evaluated in different clinical scenarios. RESULTS: A total of 1,627 hypermethylated promoter targets in the BC cell lines was identified by Illumina sequencing. The top 104 hypermethylated targets were reduced to eight genes (VAX1, KCNV1, ECEL1, TMEM26, TAL1, PROX1, SLC6A20, and LMX1A) after the urine DNA screening in a small sample size of 8 normal control and 18 BC subjects. Validation in an independent sample of 212 BC patients enabled the optimization of five methylation targets, including VAX1, KCNV1, TAL1, PPOX1, and CFTR, which was obtained in our previous study, for BC diagnosis with a sensitivity and specificity of 88.68% and 87.25%, respectively. In addition, the methylation of VAX1 and LMX1A was found to be associated with BC recurrence. CONCLUSIONS: We identified a promising diagnostic marker panel for early non-invasive detection and subsequent BC surveillance

Medico-Legal Findings, Legal Case Progression, and Outcomes in South African Rape Cases: Retrospective Review

Rachel Jewkes and colleagues examine the processing of rape cases by South African police and courts and show an association between documentation of ano-genital injuries, trials commencing, and convictions in rape cases

Realization of robust boundary modes and non-contractible loop states in photonic Kagome lattices

Corbino-geometry has well-known applications in physics, as in the design of graphene heterostructures for detecting fractional quantum Hall states or superconducting waveguides for illustrating circuit quantum electrodynamics. Here, we propose and demonstrate a photonic Kagome lattice in the Corbino-geometry that leads to direct observation of non-contractible loop states protected by real-space topology. Such states represent the "missing" flat-band eigenmodes, manifested as one-dimensional loops winding around a torus, or lines infinitely extending to the entire flat-band lattice. In finite (truncated) Kagome lattices, however, line states cannot preserve as they are no longer the eigenmodes, in sharp contrast to the case of Lieb lattices. Using a continuous-wave laser writing technique, we experimentally establish finite Kagome lattices with desired cutting edges, as well as in the Corbino-geometry to eliminate edge effects. We thereby observe, for the first time to our knowledge, the robust boundary modes exhibiting self-healing properties, and the localized modes along toroidal direction as a direct manifestation of the non-contractible loop states

Differential susceptibility to obesity between male, female and ovariectomized female mice

All authors are with the Department of Nutritional Sciences, University of Texas at Austin, Austin, Texas, USABackground: The prevalence of obesity has increased dramatically. A direct comparison in the predisposition to obesity between males, premenopausal females, and postmenopausal females with various caloric intakes has not been made. To determine the effects of sex and ovarian hormones on the susceptibility to obesity, we conducted laboratory studies with mice. To eliminate confounders that can alter body weight gain, such as age and food consumption; we used mice with the same age and controlled the amount of calories they consumed. -- Methods: We determined sex-specific susceptibility to obesity between male, non-ovariectomized female, and ovariectomized female mice. To compare susceptibility to gaining body weight between males and females, animals from each sex were exposed to either a 30% calorie-restricted, low-fat (5% fat), or high-fat (35% fat) diet regimen. To establish the role of ovarian hormones in weight gain, the ovaries were surgically removed from additional female mice, and then were exposed to the diets described above. Percent body fat and percent lean mass in the mice were determined by dual energy x-ray absorptiometry (DEXA). -- Results: In all three diet categories, male mice had a greater propensity of gaining body weight than female mice. However, ovariectomy eliminated the protection of female mice to gaining weight; in fact, ovariectomized female mice mimicked male mice in their susceptibility to weight gain. In summary, results show that male mice are more likely to become obese than female mice and that the protection against obesity in female mice is eliminated by ovariectomy. -- Conclusion: Understanding metabolic differences between males and females may allow the discovery of better preventive and treatment strategies for diseases associated with body weight such as cancer and cardiovascular disease.Nutritional [email protected]

Effects of body weight and alcohol consumption on insulin sensitivity

<p>Abstract</p> <p>Background</p> <p>Obesity is a risk factor for the development of insulin resistance, which can eventually lead to type-2 diabetes. Alcohol consumption is a protective factor against insulin resistance, and thus protects against the development of type-2 diabetes. The mechanism by which alcohol protects against the development of type-2 diabetes is not well known. To determine the mechanism by which alcohol improves insulin sensitivity, we fed water or alcohol to lean, control, and obese mice. The aim of this study was to determine whether alcohol consumption and body weights affect overlapping metabolic pathways and to identify specific target genes that are regulated in these pathways.</p> <p>Method</p> <p>Adipose tissue dysfunction has been associated with the development of type-2 diabetes. We assessed possible gene expression alterations in epididymal white adipose tissue (WAT). We obtained WAT from mice fed a calorie restricted (CR), low fat (LF Control) or high fat (HF) diets and either water or 20% ethanol in the drinking water. We screened the expression of genes related to the regulation of energy homeostasis and insulin regulation using a gene array composed of 384 genes.</p> <p>Results</p> <p>Obesity induced insulin resistance and calorie restriction and alcohol improved insulin sensitivity. The insulin resistance in obese mice was associated with the increased expression of inflammatory markers Cd68, Il-6 and Il-1α; in contrast, most of these genes were down-regulated in CR mice. Anti-inflammatory factors such as Il-10 and adrenergic beta receptor kinase 1 (Adrbk1) were decreased in obese mice and increased by CR and alcohol. Also, we report a direct correlation between body weight and the expression of the following genes: Kcnj11 (potassium inwardly-rectifying channel, subfamily J, member 11), Lpin2 (lipin2), and Dusp9 (dual-specificity MAP kinase phosphatase 9).</p> <p>Conclusion</p> <p>We show that alcohol consumption increased insulin sensitivity. Additionally, alterations in insulin sensitivity related with obesity were coupled with alterations in inflammatory genes. We provide evidence that alcohol may improve insulin sensitivity by up-regulating anti-inflammatory genes. Moreover, we have indentified potential gene targets in energy metabolic pathways and signal transducers that may contribute to obesity-related insulin resistance as well as calorie restriction and alcohol-induced insulin sensitivity.</p

Bioinformatics in China: A Personal Perspective

Biochemical Research MethodsMathematical &amp; Computational BiologySCI(E)PubMed3EDITORIAL MATERIAL4e1000020

Measurement of W+W− production in association with one jet in proton–proton collisions at sqrt(s) = 8TeV with the ATLAS detector

The production of W boson pairs in association with one jet in pp collisions at View the MathML sources=8 TeV is studied using data corresponding to an integrated luminosity of 20.3 fb−1 collected by the ATLAS detector during 2012 at the CERN Large Hadron Collider. The cross section is measured in a fiducial phase-space region defined by the presence of exactly one electron and one muon, missing transverse momentum and exactly one jet with a transverse momentum above 25 GeV and a pseudorapidity of |η|<4.5|η|<4.5. The leptons are required to have opposite electric charge and to pass transverse momentum and pseudorapidity requirements. The fiducial cross section is found to be View the MathML sourceσWWfid,1-jet=136±6(stat)±14(syst)±3(lumi) fb. In combination with a previous measurement restricted to leptonic final states with no associated jets, the fiducial cross section of WW production with zero or one jet is measured to be View the MathML sourceσWWfid,≤1-jet=511±9(stat)±26(syst)±10(lumi) fb. The ratio of fiducial cross sections in final states with one and zero jets is determined to be 0.36±0.050.36±0.05. Finally, a total cross section extrapolated from the fiducial measurement of WW production with zero or one associated jet is reported. The measurements are compared to theoretical predictions and found in good agreement