Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosomal fragmentation in dUTPase‐deficient mutants of Escherichia coli and its recombinational repair

Recent findings suggest that DNA nicks stimulate homologous recombination by being converted into double‐strand breaks, which are mended by RecA‐catalysed recombinational repair and are lethal if not repaired. Hyper‐rec mutants, in which DNA nicks become detectable, are synthetic‐lethal with recA inactivation, substantiating the idea. Escherichia coli dut mutants are the only known hyper‐recs in which presumed nicks in DNA do not cause inviability with recA, suggesting that nicks stimulate homologous recombination directly. Here, we show that dut recA mutants are synthetic‐lethal; specifically, dut mutants depend on the RecBC–RuvABC recombinational repair pathway that mends double‐strand DNA breaks. Although induced for SOS, dut mutants are not rescued by full SOS induction if RecA is not available, suggesting that recombinational rather than regulatory functions of RecA are needed for their viability. We also detected chromosomal fragmentation in dut rec mutants, indicating double‐strand DNA breaks. Both the synthetic lethality and chromosomal fragmentation of dut rec mutants are suppressed by preventing uracil excision via inactivation of uracil DNA‐glycosylase or by preventing dUTP production via inactivation of dCTP deaminase. We suggest that nicks become substrates for recombinational repair after being converted into double‐strand DNA breaks.
Differential translation in normal and adenovirus type 5-infected human cells and cell-free systems

When uninfected or adenovirus 5-infected KB cells are exposed to hypertonic medium, the incorporation of radioactive amino acids into protein decreases in both, but more severely in the uninfected cells. Although the effect of hypertonic medium on the synthesis of specific polypeptides varies, the translation of viral polypeptides as a class is less inhibited. The same patterns of proteins are synthesized regardless of the solute used in the hypertonic medium. The mechanism by which hypertonic conditions exert their effect on whole cells was investigated in K cell-free systems. It was possible to simulate the differential patterns of protein synthesis obtained in whole cells in hypertonic medium by increasing ion concentrations in cell-free extracts which are capable of initiating polypeptide chains on exogenous templates. However, in cell lysates which only elongate proteins, the same patterns were not obtained. Certain host and viral polypeptides displayed striking responses to increased ionic conditions in whole cells and cell-free systems. The synthesis of a host 44K protein, actin, appeared to be most sensitive; lower-molecular-weight proteins were fairly resistant. Among the viral proteins, the synthesis of 100K was inhibited, but most notable was the marked resistance of the synthesis of polypeptide IX. Possible mechanisms for differential synthesis and their significance are considered.
ClickLeak: Keystroke Leaks Through Multimodal Sensors in Cyber-Physical Social Networks

Public social environments are hot beds of security leaks, either they are virtual or physical. The nature of social settings allows numerous people to co-exist in the same space. This close un-bounded proximity opens up the possibility of privacy compromise in such environments. In this paper, we explore a novel and practical multi-modal side-channel keystroke recognition system, named ClickLeak, which can infer the PIN code/password entered on numeric keypad by using the commodity Wi-Fi devices. Such numeric keypads are commonly available in many public social environments. ClickLeak is built on the observation that each key input makes unique pattern of hand and finger movements, and this generates unique distortions to multi-path Wi-Fi signals. Acceleration and microphone sensors of smart phones determine the starting and ending time of keystrokes, while the time series of channel state information are analyzed to determine the keystrokes. The evaluation results have shown that with large scale data collections from public social settings, the key recognition accuracy can reach higher than 83%.
When a Boxcar Isn’t a Boxcar: Designing for Human Rights Learning

When visitors enter a boxcar, as they can at a number of Holocaust museums across the U.S., we are encouraging them to confront historical realities and put themselves in the shoes of the Nazis’ victims. But if the psychological risks of our designs outweigh their pedagogical benefits, should we simply place the boxcar out of reach? Our collaboration on research at the Illinois Holocaust Museum and Education Center (ILHMEC) kickstarted our conversations about the relationship between exhibition design and learners’ emotional and intellectual responses. Mann had already headed the development team for Lied Discovery
Association studies and gene expression analyses of the DISC1‐interacting molecules, pericentrin 2 (PCNT2) and DISC1‐binding zinc finger protein (DBZ), with schizophrenia and with bipolar disorder

Disrupted‐in‐Schizophrenia 1 (DISC1) and its molecular cascade have been implicated in the pathophysiology of major psychoses. Previously, we identified pericentrin 2 (PCNT2) and DISC1‐binding zinc finger protein (DBZ) as binding partners of DISC1; further, we observed elevated expression of PCNT2 in the postmortem brains and in the lymphocytes of bipolar disorder patients, compared to controls. Here, we examined the association of PCNT2 with schizophrenia in a case–control study of Japanese cohorts. We also examined the association of DBZ with schizophrenia and with bipolar disorder, and compared the mRNA levels of DBZ in the postmortem brains of schizophrenia, bipolar and control samples. DNA from 180 schizophrenia patients 201 controls were used for the association study of PCNT2 and DBZ with schizophrenia. Association of DBZ with bipolar disorder was examined in DNA from 238 bipolar patients and 240 age‐ and gender‐matched controls. We observed significant allelic and genotypic associations of the PCNT2 SNPs, rs2249057, rs2268524, and rs2073380 (Ser/Arg) with schizophrenia; the association of rs2249057 (P = 0.002) withstand multiple testing correction. Several two SNP‐ and three SNP‐haplotypes showed significant associations; the associations of haplotypes involving rs2249057 withstand multiple testing correction. No associations were observed for DBZ with schizophrenia or with bipolar disorder; further, there was no significant difference between the DBZ mRNA levels of control, schizophrenia and bipolar postmortem brains. We suggest a possible role of PCNT2 in the pathogenesis of schizophrenia. Abnormalities of PCNT2, the centrosomal protein essential for microtubule organization, may be suggested to lead to neurodevelopmental abnormalities. © 2009 Wiley‐Liss, Inc.
Reporting about disability evaluation in European countries

Abstract Purpose: To compare the official requirements of the content of disability evaluation for social insurance across Europe and to explore how the International Classification of Functioning, Disability and Health is currently applied, using the rights and obligations of people with disabilities towards society as frame of reference. Methods: Survey. We used a semi-structured questionnaire to interview members of the European Union of Medicine in Assurance and Social Security (EUMASS), who are central medical advisors in social insurance systems in their country. We performed two email follow-up rounds to complete and verify responses. Results: Fifteen respondents from 15 countries participated. In all countries, medical examiners are required to report about a claimant’s working capacity and prognosis. In 14 countries, medical reports ought to contain information about socio-medical history and feasible interventions to improve the claimant’s health status. The format of medical reporting on working capacity varies widely (free text, semi- and fully structured reports). One country makes a reference to the ICF in their reports on working capacity, others consider doing so. Conclusion: Official requirements on medical reporting about disability in social insurance across Europe follow the frame of four features: work capacity, socio-medical history, feasibility of intervention and prognosis of disability. There is an increasing trend to make formal or informal reference to the ICF in the reports about working capacity. The four features and the ICF may provide common references across countries to describe disability evaluation, facilitating national and international research. Implications for Rehabilitation Reporting about disability in social insurance in different countries is about work capacity, social medical history, feasibility of intervention and prognosis of disability. Formats of reporting on work capacity vary among countries, from free text to semi-structured report forms to fully structured and scaled report forms of working capacity. The ICF could serve as a reference for describing work capacity, provided the ICF contains all necessary categories.
OpenACC Cache Directive: Opportunities and Optimizations

OpenACC's programming model presents a simple interface to programmers, offering a trade-off between performance and development effort. OpenACC relies on compiler technologies to generate efficient code and optimize for performance. Among the difficult to implement directives, is the cache directive. The cache directive allows the programmer to utilize accelerator's hardware- or software-managed caches by passing hints to the compiler. In this paper, we investigate the implementation aspect of cache directive under NVIDIA-like GPUs and propose optimizations for the CUDA backend. We use CUDA's shared memory as the software-managed cache space. We first show that a straightforward implementation can be very inefficient, and downgrade performance. We investigate the differences between this implementation and hand-written CUDA alternatives and introduce the following optimizations to bridge the performance gap between the two: i) improving occupancy by sharing the cache among several parallel threads and ii) optimizing cache fetch and write routines via parallelization and minimizing control flow. We present compiler passes to apply these optimizations. Investigating three test cases, we show that the best cache directive implementation can perform very close to hand-written CUDA equivalent and improve performance up to 2.18X (compared to the baseline OpenACC.)
Family labor supply and aggregate saving

I study the impact of idiosyncratic risk on savings and employment in a small open economy populated by two-member families. Families incur a fixed cost of participation when both members are employed. Because of market incompleteness and information asymmetries, this cost coupled with labor market frictions can generate multiple equilibria. In particular, there might be one equilibrium with high employment and low saving and another one with low employment and high saving. The model predicts that aggregate saving and employment rates are negatively correlated across countries. I present empirical evidence that supports the general equilibrium prediction of the model.
Assessing Comorbidity Using Claims Data: An Overview

Comorbidity, additional disease beyond the condition under study that increases a patient’s total burden of illness, is one dimension of health status. For investigators working with observational data obtained from administrative databases, comorbidity assessment may be a useful and important means of accounting for differences in patients’ underlying health status. There are multiple ways of measuring comorbidity. This paper provides an overview of current approaches to and issues in assessing comorbidity using claims data, with a particular focus on established indices and the SEER-Medicare database. In addition, efforts to improve measurement of comorbidity using claims data are described, including augmentation of claims data with medical record, patient self-report, or health services utilization data; incorporation of claims data from sources other than inpatient claims; and exploration of alternative conditions, indices, or ways of grouping conditions. Finally, caveats about claims data and areas for future research in claims-based comorbidity assessment are discussed. Although the use of claims databases such as SEER-Medicare for health services and outcomes research has become increasingly common, investigators must be cognizant of the limitations of comorbidity measures derived from these data sources in capturing and controlling for differences in patient health status. The assessment of comorbidity using claims data is a complex and evolving area of investigation.
High Malaria Transmission Intensity in a Village Close to Yaounde, the Capital City of Cameroon

Abstract A 2-yr longitudinal malaria study was undertaken in a suburb of Yaounde, the capital city of Cameroon, in the village of Simbock, ≈2 km from the city limits. This study allowed assessment of malaria transmission intensity and dynamics in this region before implementation of pyrethroid impregnated bed nets through the national vector control program. Anophelines were captured on human volunteers by pyrethrum spray collections and in resting sites outdoors. Malaria vectors were Anopheles funestus Giles, Anopheles gambiae s.s. Giles (M and S forms), Anopheles moucheti Evans, and Anopheles nili Theobald. An. moucheti was the most abundant mosquito captured during the study, accounting for >54% of total anophelines caught. The annual Plasmodium falciparum Welch entomological inoculation rates measured by enzyme-linked immunosorbent assay were 277 infected bites per human for the first year and 368 for the second year. An. gambiae s.s. , An. funestus, An. moucheti, and An. nili were responsible for 23.8%, 26.8%, 39.2%, and 10.2% of malaria transmission, respectively. Malaria transmission is perennial throughout the year. All these vectors were highly anthropophagous because only two out of 566 mosquitoes blood-meal tested were not taken on humans.
Expectation and Entropy in Spoken Word Recognition: Effects of Age and Hearing Acuity

Background/Study Context: Older adults, especially those with reduced hearing acuity, can make good use of linguistic context in word recognition. Less is known about the effects of the weighted distribution of probable target and nontarget words that fit the sentence context (response entropy). The present study examined the effects of age, hearing acuity, linguistic context, and response entropy on spoken word recognition. Methods: Participants were 18 older adults with good hearing acuity (M age = 74.3 years), 18 older adults with mild-to-moderate hearing loss (M age = 76.1 years), and 18 young adults with age-normal hearing (M age = 19.6 years). Participants heard sentence-final words using a word-onset gating paradigm, in which words were heard with increasing amounts of onset information until they could be correctly identified. Degrees of context varied from a neutral context to a high context condition. Results: Older adults with poor hearing acuity required a greater amount of word onset information for recognition of words when heard in a neutral context compared with older adults with good hearing acuity and young adults. This difference progressively decreased with an increase in words’ contextual probability. Unlike the young adults, both older adult groups’ word recognition thresholds were sensitive to response entropy. Response entropy was not affected by hearing acuity. Conclusion: Increasing linguistic context mitigates the negative effect of age and hearing loss on word recognition. The effect of response entropy on older adults’ word recognition is discussed in terms of an age-related inhibition deficit.
Making Sense of the Dollars Spent at Farmers’ Markets

The habits, preferences and demographics of consumers at farmers’ markets are topics of interest as the number of markets burgeon across North America. This study, using a survey (via interview), researches five markets near Vancouver, British Columbia, focusing on factors associated with spending. The results reveal that spending is significantly related to frequency of shopping, type of products purchased, preferences about buying organic, parking habits, and demographics such as age, education level, ethnicity, family composition and home ownership. The study also shows that Vancouver-area farmers’ market shoppers are not significantly different from those elsewhere—they too tend to be older, well-educated and disproportionately Caucasian. Results yield valuable practical strategies for market managers.
Isolation and characterization of ropA homologous genes from Rhizobium leguminosarum biovars viciae and trifolii

ropA encodes a 36-kDa outer membrane protein of Rhizobium leguminosarum bv. viciae strain 248 which constitutes the low-M(r) part of antigen group III (R.A. de Maagd, I.H.M. Mulders, H.C.J. Canter Cremers, B.J.J. Lugtenberg, J. Bacteriol. 174:214-221, 1992). We observed that genes homologous to ropA are present in strain 248 as well as in other R. leguminosarum strains, and we describe the cloning and characterization of two of these genes. Sequencing of a 2.2-kb Bg/II fragment from R. leguminosarum bv. viciae strain 248 that hybridizes with ropA revealed one large open reading frame of 1,074 bp encoding a mature protein of 38.096 kDa. Homology between this gene and ropA is 91.8% on the DNA level. Homology on the amino acid level is only 69.9% as a result of a frameshift. On the basis of homology and immunochemical characteristics, we conclude that this gene encodes the high-M(r) part of the outer membrane protein antigen group III that is repressed during symbiosis. We named this gene ropA2. The second gene that we cloned was the ropA homologous gene of R. leguminosarum bv. trifolii strain LPR5020. Except for amino acid 43, the N-terminal part of the corresponding protein appeared to be identical to the first 51 amino acids of RopA of strain 248. The transcription start sites of both genes were determined, and the promoter regions were compared with that of ropA of strain 248. No clear consensus sequence could be deduced. The relationship of ropA and ropA2 of R. leguminosarum bv. viciae strain 248 with two similar genes from Brucella abortus is discussed.
Vegetation attenuation of the very low grazing angle radar pulses by coconut trees at 5.3GHz

The vertically polarized radar pulses coconut trees vegetation attenuation at 5.3GHz is investigated by a series of different tests from 3km to 30km away the transmitter near HaiKou city of HaiNan province of China with very low grazing angles in winter. The uniform path loss (UPL) model is adopted and verified as an effective method for radar pulse vegetation attenuation theoretical analyses by taking the modified radar pulses illumination area as the mean transmission cross section.
Managing External Volatility: Central Bank Options in Low-Income Countries

flexibility of exchange rates since the late 1980s. Table 1 documents this for Sub-Saharan Africa (SSA), where outside of monetary unions there has been a strong trend towards the adoption of intermediate or more flexible regimes. In many cases the move to greater exchange rate flexibility accompanied a concerted effort to establish monetary aggregates as inflation anchors, via the application of tight limits on budgetary financing and a strengthening of the institutional independence of the central bank. As a result of these developments, the majority of non-CFA central banks in SSA now publicly embrace a market-determined exchange rate. Monetary policy is formally conducted within a variant of reserve-money programming, with an eye on an eventual transition to formal inflation targeting. In practice, however, the move to exchange rate flexibility has been fairly cautious, both by comparison with public pronouncements and by the standards of the more decisive legacy of the period, the abandonment of tight exchange controls and disequilibrium exchange rates.
G protein‐coupled receptor kinase‐3‐deficient mice exhibit WHIM syndrome features and attenuated inflammatory responses

Chemokine receptor interactions coordinate leukocyte migration in inflammation. Chemokine receptors are GPCRs that when activated, are phosphorylated by GRKs to turn off G protein‐mediated signaling yet recruit additional signaling machinery. Recently, GRK3 was identified as a negative regulator of CXCL12/CXCR4 signaling that is defective in human WHIM syndrome. Here, we report that GRK3−/− mice exhibit numerous features of human WHIM, such as impaired CXCL12‐mediated desensitization, enhanced CXCR4 signaling to ERK activation, altered granulocyte migration, and a mild myelokathexis. Moreover, GRK3−/− protects mice from two acute models of inflammatory arthritis (K/BxN serum transfer and CAIA). In these granulocyte‐dependent disease models, protection of GRK3−/− mice is mediated by retention of cells in the marrow, fewer circulating granulocytes in the peripheral blood, and reduced granulocytes in the joints during active inflammation. In contrast to WHIM, GRK3−/− mice have minimal hypogammaglobulinemia and a peripheral leukocytosis with increased lymphocytes and absent neutropenia. Thus, we conclude that the loss of GRK3‐mediated regulation of CXCL12/CXCR4 signaling contributes to some, but not all, of the complete WHIM phenotype and that GRK3 inhibition may be beneficial in the treatment of inflammatory arthritis.
Upstream genetic variant near INSIG2, influences response to carnitine supplementation in bipolar patients with valproate-induced weight gain

Background: The protein product of INSIG2 is involved in cholesterol and triglyceride metabolism and homeostasis. Variation at rs7566605 near the gene INSIG2 has been associated with increased BMI. Objective: To evaluate the effect of rs7566605/INSIG2 genotype on the ability of valproate-treated bipolar patients (BMI ≥ 25 kg/m2) to lose weight using carnitine supplementation during a 26-week lifestyle intervention study. Design: Forty-eight bipolar patients with clinically significant treatment emergent weight gain were genotyped at the rs7566605 SNP. Participants were randomised to l-carnitine (15 mg/kg/day) or placebo for 26 weeks in conjunction with a moderately energy restricted, low-fat diet. Weight and body fat percent were measured fortnightly. Waist circumference measurements and dual-energy X-ray absorptiometry were used to assess changes in body composition. Obesity-related biomarkers were measured at baseline and 26 weeks. Results: There was a significant interaction between rs7566605/INSIG2 genetic status and treatment with carnitine or placebo. Carnitine had no significant effect on body composition measures in G allele homozygous patients who lost between 0.97 and 2.23 kg of fat. However C allele carriers on average gained 2.28 kg when given a placebo. Carnitine supplementation in this group enabled average weight loss of 2.22 kg of fat (p = 0.01). Approximately half of this mass was in the vital truncal compartment (p = 0.002). Bioinformatic analysis detected that the SNP lies in a highly conserved 336 bp sequence which potentially affects INSIG2 gene expression. Conclusions: C-carriers at rs7566605, possibly regulating the homeostasis gene INSIG2, lost significantly less weight in this lifestyle intervention study. This effect was reversed by carnitine supplementation.