Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Molecular Phenotyping to Guide Improvements in the Histologic Diagnosis of T Cell–Mediated Rejection

Recognition that some lesions typical of T cell–mediated rejection (TCMR) also occur in antibody‐mediated rejection requires revision of the histologic TCMR definition. To guide this process, we assessed the relative importance of various lesions and the performance of new histology diagnostic algorithms, using molecular TCMR scores as histology‐independent estimates of true TCMR. In 703 indication biopsies, random forest analysis and logistic regression indicated that interstitial infiltrate (i‐lesions) and tubulitis (t‐lesions) were the key histologic predictors of molecular TCMR, with arteritis (v‐lesions) having less importance. Histology predicted molecular TCMR more accurately when diagnoses were assigned by strictly applying the Banff rules to the lesion scores and redefining isolated v‐lesion TCMR. This improved prediction from area under the curve (AUC) 0.70 with existing rules to AUC 0.80. Further improvements were achieved by introducing more categories to reflect inflammation (AUC 0.84), by summing the lesion scores (AUC 0.85) and by logistic regression (AUC 0.90). We concluded that histologic assessment of TCMR can be improved by placing more emphasis on i‐ and t‐lesions and incorporating new algorithms for diagnosis. Nevertheless, some discrepancies between histologic and molecular diagnoses persist, partially due to the inherent nonspecificity of i‐ and t‐lesions, and molecular methods will be required to help resolve these cases.
Is “Good Enough” Good Enough when Hedging Agricultural Commodities?

This paper explores the returns to grain producers and processors of expending efforts to determine hedge ratios. We use cash and futures prices from Barchart.com and multi-location cash prices from the Daily Grain Review to determine if location-specific hedge ratios are superior to hedge ratios estimated for a central location then used for hedging at the specific location. We find that the price-risk management capabilities of single location hedge ratios computed the Barchart data perform well in hedging grains at other locations. This suggests that producers and processors should not invest heavily in determining precise hedge ratios that apply to a particular location. In other words, “good enough” hedge ratios are in fact good enough.
Incentive Contracts and Status-Concerned Agents

Abstract Traditionally in economics the actions of agents have been viewed as driven exclusively by individuals' interest in their own wealth. Nonetheless experimental evidence shows that agents enjoy being richer than their peers or, in other words, agents are interested in their status within a group. In this work I derive the optimal linear contract in a moral hazard problem where agents are risk averse and are concerned about how much they are compensated relative to their colleagues. I show that in the presence of such relative wealth concerns: 1. ) It is optimal for the principal to offer a compensation schedule linked to the overall firm or team performance, even when each agent's performance is observable, contractible and independent on the actions taken by his/her colleagues; 2. ) Relative Performance Evaluation is less desirable for the principal.
Individualized Implant-Based Reconstruction of Poland Syndrome Breast and Soft Tissue Deformities

Background:Poland syndrome encompasses a constellation of congenital chest wall, breast, and upper-extremity deformities, which present a significant reconstructive challenge for the plastic surgeon. The broad range of chest wall and breast anomalies has led to an equally broad variety of surgical solutions. Often, however, initial attempts at surgical correction fall short because of failure to identify the best reconstructive option for an individual's particular deformity. Methods:In a retrospective series of 29 patients, we report our institution's experience with reconstructing breast and chest contour deformities associated with Poland syndrome. We also present a review of the literature. Results:The breast and chest wall deformities associated with Poland syndrome can be effectively treated in an algorithmic, individualized fashion. Conclusions:We propose an algorithmic approach to the patient with a Poland syndrome chest wall and breast deformity.
Reduction of intermodulation distortion with harmonic injection for wideband traveling-wave tubes

Large signal studies on octave bandwidth traveling-wave tubes show that significant improvements in tube linearity can be achieved with harmonic injection, in addition to efficiency enhancements and suppression of parasitic harmonic signals. In multisignal operation considerable reduction of the intermodulation distortion can be expected with this scheme. This requires that the injected harmonic signals be optimized in amplitude and phase with respect to the fundamental signals. In practice the harmonic signals can be generated with an octave bandwidth driver tube, and a harmonic conditioner can be designed to optimize the injection conditions. With two and four simultaneous signals improvements in intermodulation distortion by about 6 dB have been demonstrated at saturation with intermodulation levels of approximately 18 dB below the signals.
Action of Protein Disulfide Isomerase on Proinsulin Exit from Endoplasmic Reticulum of Pancreatic β-Cells*

Background: We have examined the effect of PDI knockdown in pancreatic β-cells. Results: Upon knockdown, proinsulin oxidation to form native disulfide bonds is enhanced and accompanied by improved exit from the ER with increased total insulin secretion. Conclusion: We hypothesize that PDI exhibits unfoldase activity for proinsulin. Significance: Unexpectedly, PDI increases retention of proinsulin within the ER of pancreatic β-cells. For insulin synthesis, the proinsulin precursor is translated at the endoplasmic reticulum (ER), folds to include its three native disulfide bonds, and is exported to secretory granules for processing and secretion. Protein disulfide isomerase (PDI) has long been assumed to assist proinsulin in this process. Herein we have examined the effect of PDI knockdown (PDI-KD) in β-cells. The data establish that upon PDI-KD, oxidation of proinsulin to form native disulfide bonds is unimpaired and in fact enhanced. This is accompanied by improved proinsulin exit from the ER and increased total insulin secretion, with no evidence of ER stress. We provide evidence for direct physical interaction between PDI and proinsulin in the ER of pancreatic β-cells, in a manner requiring the catalytic activity of PDI. In β-cells after PDI-KD, enhanced export is selective for proinsulin over other secretory proteins, but the same effect is observed for recombinant proinsulin trafficking upon PDI-KD in heterologous cells. We hypothesize that PDI exhibits unfoldase activity for proinsulin, increasing retention of proinsulin within the ER of pancreatic β-cells.
Mobile Time­Space - Arena for New Kinds of Social Actions

At the millennium, when I became involved with research on the social dimensions and consequences of mobile technologies, I was struck by a paradox. An air of enthusiasm surrounded the mobile world. Both ordinary people and industries were thrilled by the new mobile possibilities. The relatively reliable statistics of mobile operators, however, showed that people were using mobile phones just five minutes a day on average in Finland – one of the mobile technology forerunners at that point mainly talking to each other, sending some text messages, and not really much more (Nurmela 2001). As the enthusiasm seemed sincere, I had to ask what was so revolutionary about these five minutes a day. I have been asking this question ever since.
Exploiting ontology graph for predicting sparsely annotated gene function

Motivation: Systematically predicting gene (or protein) function based on molecular interaction networks has become an important tool in refining and enhancing the existing annotation catalogs, such as the Gene Ontology (GO) database. However, functional labels with only a few (<10) annotated genes, which constitute about half of the GO terms in yeast, mouse and human, pose a unique challenge in that any prediction algorithm that independently considers each label faces a paucity of information and thus is prone to capture non-generalizable patterns in the data, resulting in poor predictive performance. There exist a variety of algorithms for function prediction, but none properly address this ‘overfitting’ issue of sparsely annotated functions, or do so in a manner scalable to tens of thousands of functions in the human catalog. Results: We propose a novel function prediction algorithm, clusDCA, which transfers information between similar functional labels to alleviate the overfitting problem for sparsely annotated functions. Our method is scalable to datasets with a large number of annotations. In a cross-validation experiment in yeast, mouse and human, our method greatly outperformed previous state-of-the-art function prediction algorithms in predicting sparsely annotated functions, without sacrificing the performance on labels with sufficient information. Furthermore, we show that our method can accurately predict genes that will be assigned a functional label that has no known annotations, based only on the ontology graph structure and genes associated with other labels, which further suggests that our method effectively utilizes the similarity between gene functions. Availability and implementation: https://github.com/wangshenguiuc/clusDCA. Contact: jianpeng@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Doppler Echocardiographic Measurements in Normal Chinese Adults (EMINCA): a prospective, nationwide, and multicentre study.

AIMS Currently, available Doppler echocardiographic reference values are derived mainly from North American and European population studies, which may not applicable to the Chinese population. We aimed to establish normal reference values of Doppler echocardiographic parameters in a nationwide, population-based cohort of healthy Han Chinese adults. METHODS AND RESULTS A total of 1394 qualified healthy subjects (mean age 47.3 ± 16.0 years, 678 men) were enrolled at 43 collaborating laboratories, 37 transvalvular flow and tissue Doppler parameters were obtained, and the impacts of gender and age on each parameter were analysed. Significant differences were found between men and women in 48.6% (18/37) of the parameters analysed, and among different age groups in 83.8% (31/37) of the parameters in men and in 86.5% (32/37) of the parameters in women. CONCLUSIONS Normal reference values of Doppler echocardiographic parameters were established for the first time in a nationwide, population-based cohort of healthy Han Chinese adults. Since most of these parameters differed by gender and/or age, reference values specified for gender and age should be recommended in clinical practice.
Cumulative Forces Behind the Economic Development in East Asia and Sri Lanka's Development Experiences

This paper attempts to identify a process of cumulative reinforcements that sustained pro-growth state orientations and the other participants’ motives for collaboration during the post World War II economic development East Asia. The process is elaborated in terms of the five parties who were engaged in it: political leader; ruling party; bureaucrats; industrialists; and aid donors/loan providers. Accordingly, the Developmental State is viewed as an entity that simultaneously governed the market and influenced by the growth process that it had accelerated. This helps us answer some of the criticisms leveled at the Developmental State literature such as: (a) its inadequate attention paid to where the pro-growth orientations came from; and (b) the Developmental State is an autonomous and time-less structure. In a latter part of the paper, the development experiences of Sri Lanka, a country from a totally different environment, is examined in the light of the framework developed in the first few parts.
Epidemiology of Cyberbullying across Europe: Differences between Countries and Genders

Epidemiological studies on the prevalence of cyberbullying and cybervictimization in different countries, using the same procedure and the same measures, are of relevance in understanding differences in results that are not due to methodological factors. The current study was conducted in 8 European countries (Bulgaria, Cyprus, France, Greece, Hungary, Italy, Poland, and Spain), involving a total of 4,847 students, using an online anonymous questionnaire (the Tabby online questionnaire). The results were analyzed by comparing differences between countries and between genders. Cyberbullying and cybervictimization were most prevalent in Bulgaria and Hungary and least prevalent in Spain. Boys committed more cyberbullying than girls in all countries, but there were no overall gender differences in cybervictimization. However, girls were more often cybervictims in four countries and boys were more often cybervictims in the other four countries. The results are discussed with regard to the importance of cross-national studies of cyberbullying and cybervictimization and the use of online data collection in order to reduce methodological
An electrochemical sensor for quantitative analysis of Rhesus D antibodies in blood

The Hemolytic Disease of the Fetus and Newborn (HDFN), if untreated, can have severe consequences on baby's health, eventually causing death. Prevention and diagnosis of pregnancies at risk of HDFN consists in quantitative analysis in hospital every 2–4 weeks of blood group antibodies in maternal serum. The most important antibodies to be monitored are anti-Rhesus D (or anti-RhD) ones. Nowadays several portable systems for different healthcare applications have been developed towards decentralization of diagnosis thanks to the enormous advances in electrochemical biosensing. Home-monitoring of pregnancies at risk of HDFN could significantly improve patients' life quality. Here we demonstrate for the first time label-free quantitative detection of anti-RhD antibodies by means of electrochemical impedance spectroscopy (EIS), suitable for integration within a complete portable device. The specificity of the sensor was also proved.
PRAM-a power ramping controller for TDMA systems in digital mobile telecom applications

Modern digital cellular or cordless telephone standards like GSM or DECT share frequency bands among several users by time division multiple access (TDMA). This approach necessitates the power amplifier being rapidly ramped up and down for transmit bursts. To balance the trade-off between quick turn-on and turnoff and spurious spectral emissions, the recommendations define strict templates into which the output power must fit. This integrated circuit is fabricated in a standard CMOS technology with self-aligned contacts for all control functions for RF power amplifiers in bipolar or GaAs technology for the GSM, DCS1800 or PCN1900 standards. The device may be used as a stand alone component but can also be included on a VLSI as a library block.
Collaborative Conceptual Modeling: Share, Search and Reuse

Within the Qualitative Reasoning community there is a desire to collaborate by integrating work and reusing parts of existing models. Although there has been much attention for the knowledge representation formalisms required for these tasks, activities performed by knowledge engineers such as copying model parts, searching for relevant models, and sharing intermediate modeling results are often not supported by existing modeling tools. This paper presents a set of new features in the Garp3 qualitative reasoning and modeling workbench to support these activities.
Nonphosphorylated Human La Antigen Interacts with Nucleolin at Nucleolar Sites Involved in rRNA Biogenesis

ABSTRACT La is a RNA-binding protein implicated in multiple pathways related to the production of tRNAs, ribosomal proteins, and other components of the translational machinery (D. J. Kenan and J. D. Keene, Nat. Struct. Mol. Biol. 11 :303-305, 2004). While most La is phosphorylated and resides in the nucleoplasm, a fraction is in the nucleolus, the site of ribosome production, although the determinants of this localization are incompletely known. In addition to its conserved N-terminal domain, human La harbors a C-terminal domain that contains an atypical RNA recognition motif and a short basic motif (SBM) adjacent to phosphoserine-366. We report that nonphosphorylated La (npLa) is concentrated in nucleolar sites that correspond to the dense fibrillar component that harbors nascent pol I transcripts as well as fibrillarin and nucleolin, which function in early phases of rRNA maturation. Affinity purification and native immunoprecipitation of La and fluorescence resonance energy transfer in the nucleolus reveal close association with nucleolin. Moreover, La lacking the SBM does not localize to nucleoli. Lastly, La exhibits SBM-dependent, phosphorylation-sensitive interaction with nucleolin in a yeast two-hybrid assay. The data suggest that interaction with nucleolin is, at least in part, responsible for nucleolar accumulation of La and that npLa may be involved in ribosome biogenesis.
That Man Behind the Curtain: Investigating the Sexual Online Dating Behavior of Men Who Have Sex With Men but Hide Their Same-Sex Sexual Attraction in Offline Surroundings

ABSTRACT This study investigates how men who have sex with men (MSM) use chat and dating sites based on theories of stigma-related offline behavior and online self-disclosure. We hypothesize that hidden MSM (those who self-label as heterosexual or who hide their same-sex sexual attraction from family, friends, acquaintances, or a female romantic partner) differ from open MSM in how they behave on gay chat and dating sites and in offline gay venues. Drawing on a survey of 12,002 MSM, we show that hidden MSM tend to mask their identity on gay chat and dating sites while avoiding offline gay venues. They also focus more strongly on online sexual activities (e.g., masturbating during online chats) when using gay chat and dating sites. However, they spend the same amount of time on these sites, and they use them to initiate offline sexual encounters as often and as fast as open MSM.
Phase I trial of oral green tea extract in adult patients with solid tumors.

PURPOSE This trial was designed to determine the maximum-tolerated dose, toxicity, and pharmacology of oral green tea extract (GTE) once daily or three times daily. PATIENTS AND METHODS Cohorts of three or more adult cancer patients were administered oral GTE with water after meals one or three times daily for 4 weeks, to a maximum of 6 months, depending on disease response and patient tolerance. Pharmacokinetic analyses were encouraged but optional. RESULTS Dose levels of 0.5 to 5.05 g/m(2) qd and 1.0 to 2.2 g/m(2) tid were explored. A total of 49 patients were studied. PATIENT CHARACTERISTICS median age, 57 years (range, 27 to 77 years); 23 patients were women (47%); 98% had a Zubrod PS of 1%; 98% had PS of 1; and 21 had non-small-cell lung, 19 had head & neck cancer, three had mesothelioma, and six had other. Mild to moderate toxicities were seen at most dose levels and promptly reversed on discontinuation of GTE. Dose-limiting toxicities were caffeine related and included neurologic and gastrointestinal effects. The maximum-tolerated dose was 4.2 g/m(2) once daily or 1.0 g/m(2) three times daily. No major responses occurred; 10 patients with stable disease completed 6 months of GTE. Pharmacokinetic analyses found accumulation of caffeine levels that were dose dependent, whereas epigallocatechin gallate levels did not accumulate nor appear dose related. CONCLUSION A dose of 1.0 g/m(2) tid (equivalent to 7 to 8 Japanese cups [120 mL] of green tea three times daily) is recommended for future studies. The side effects of this preparation of GTE were caffeine related. Oral GTE at the doses studied can be taken safely for at least 6 months.
Effects of TWIN-OF-EYELESS on Clock Gene Expression and Central-Pacemaker Neuron Development in Drosophila

Circadian oscillators are autonomous molecular rhythms that reside in cells to align whole-organism physiology and behavior to the 24-h day. In flies, as in mammals, the oscillator operates in cells that coexpress CLOCK (CLK) and CYCLE (CYC). Recent work in Drosophila has shown that CLK is unique in its ability to generate heterologous oscillators, indicating that Clk gene expression defines the circadian cell fate. Here, using standard in vitro and in vivo techniques, we show that TWIN-OF-EYELESS (TOY; dPax6) regulates Clk expression in small ventrolateral neurons (s-LNvs) that coordinate sleep-wake cycles. Crucially, toy binds multiple sites at the Clk locus, is expressed independent of CLK-CYC in LNvs, regulates CLK protein levels under optimal photoperiodic conditions, and sets clock-speed during endogenous free-run. Furthermore, TOY is necessary for the onset of Clk expression in LNvs during embryogenesis. We propose that TOY contributes to a transcription complex that functions upstream of the oscillator to promote Clk expression in s-LNvs.
Some Notes on the Rationality Model

In this set of notes on the importance of integrating the geometric mean into the mainstream of financial reasoning with regard to risky ventures that might fail we discuss some forces which are tending to make financial markets conform to the rationality hypothesis, present a model that is particularly useful in analyzing investments that are too big to be prudently undertaken by one decision-making unit, show the model's applicability to a number of decision areas such as large scale R & D investment, and indicate some perils and pitfalls in using wealth maximizing equations to guard against financial ruin.
How Autonomy Impacts Performance and Satisfaction: Results From a Study With Spinal Cord Injured Subjects Using an Assistive Robot

We report a small dual cohort pilot study with traumatic spinal cord injured (SCI) subjects designed to investigate the utility of a wheelchair-mounted robotic arm for these subjects. The UCF-MANUS, a vision-based 6DOF assistive robotic arm, has been designed to aid individuals with upper limb extremities to complete tasks of daily living that they would otherwise be unable to complete themselves. Pick-and-place IADL tasks were designed and ten (10) users post-SCI were selected under IRB guidelines to be trained and tested with the system for 1 to 2 h weekly over a period of three weeks. During this time, they controlled the robot either through a manual or an autonomous (supervised) mode of operation. Baseline characteristics (pre-study), quantitative performance metrics (during study), and psychometrics (post-study) were obtained and statistically analyzed to test a set of hypotheses related to performance and satisfaction with the two control modes. At the end of the study, both the autonomous and the manual mode had comparable task completion times while user effort required for operating the robot in autonomous mode was significantly less than that for the manual mode. However, the autonomous mode failed to commensurately raise the user's level of satisfaction. Over the three-week study, the manual mode users showed a pronounced learning effect in terms of reducing mean task completion time and number of commands while the auto mode users showed improvement in terms of reduction of variability. Based on qualitative feedback and quantitative results, possible directions for system design are presented to concurrently achieve better performance and satisfaction outcomes.