Miracle-dz/UniFAR-FTUs huggingface dataset:
sbcB15 and ΔsbcB Mutations Activate Two Types of RecF Recombination Pathways in Escherichia coli

ABSTRACT Escherichia coli cells with mutations in recBC genes are defective for the main RecBCD pathway of recombination and have severe reductions in conjugational and transductional recombination, as well as in recombinational repair of double-stranded DNA breaks. This phenotype can be corrected by suppressor mutations in sbcB and sbcC(D) genes, which activate an alternative RecF pathway of recombination. It was previously suggested that sbcB15 and ΔsbcB mutations, both of which inactivate exonuclease I, are equally efficient in suppressing the recBC phenotype. In the present work we reexamined the effects of sbcB15 and ΔsbcB mutations on DNA repair after UV and γ irradiation, on conjugational recombination, and on the viability of recBC (sbcC) cells. We found that the sbcB15 mutation is a stronger recBC suppressor than ΔsbcB, suggesting that some unspecified activity of the mutant SbcB15 protein may be favorable for recombination in the RecF pathway. We also showed that the xonA2 mutation, a member of another class of ExoI mutations, had the same effect on recombination as ΔsbcB, suggesting that it is an sbcB null mutation. In addition, we demonstrated that recombination in a recBC sbcB15 sbcC mutant is less affected by recF and recQ mutations than recombination in recBC ΔsbcB sbcC and recBC xonA2 sbcC strains is, indicating that SbcB15 alleviates the requirement for the RecFOR complex and RecQ helicase in recombination processes. Our results suggest that two types of sbcB-sensitive RecF pathways can be distinguished in E. coli, one that is activated by the sbcB15 mutation and one that is activated by sbcB null mutations. Possible roles of SbcB15 in recombination reactions in the RecF pathway are discussed.
Low-pass filters and differential tympanal tuning in a paleotropical bushcricket with an unusually low frequency call

SUMMARY Low-frequency sounds are advantageous for long-range acoustic signal transmission, but for small animals they constitute a challenge for signal detection and localization. The efficient detection of sound in insects is enhanced by mechanical resonance either in the tracheal or tympanal system before subsequent neuronal amplification. Making small structures resonant at low sound frequencies poses challenges for insects and has not been adequately studied. Similarly, detecting the direction of long-wavelength sound using interaural signal amplitude and/or phase differences is difficult for small animals. Pseudophylline bushcrickets predominantly call at high, often ultrasonic frequencies, but a few paleotropical species use lower frequencies. We investigated the mechanical frequency tuning of the tympana of one such species, Onomarchus uninotatus, a large bushcricket that produces a narrow bandwidth call at an unusually low carrier frequency of 3.2 kHz. Onomarchus uninotatus, like most bushcrickets, has two large tympanal membranes on each fore-tibia. We found that both these membranes vibrate like hinged flaps anchored at the dorsal wall and do not show higher modes of vibration in the frequency range investigated (1.5–20 kHz). The anterior tympanal membrane acts as a low-pass filter, attenuating sounds at frequencies above 3.5 kHz, in contrast to the high-pass filter characteristic of other bushcricket tympana. Responses to higher frequencies are partitioned to the posterior tympanal membrane, which shows maximal sensitivity at several broad frequency ranges, peaking at 3.1, 7.4 and 14.4 kHz. This partitioning between the two tympanal membranes constitutes an unusual feature of peripheral auditory processing in insects. The complex tracheal shape of O. uninotatus also deviates from the known tube or horn shapes associated with simple band-pass or high-pass amplification of tracheal input to the tympana. Interestingly, while the anterior tympanal membrane shows directional sensitivity at conspecific call frequencies, the posterior tympanal membrane is not directional at conspecific frequencies and instead shows directionality at higher frequencies.
Heatstroke‐Induced Cerebral Ischemia and Neuronal Damage

Experiments were carried out to ascertain whether the levels of brain monoamines and cytokines are involved in the heatstroke-induced cerebral ischemia and neuronal damage. Heatstroke was induced by exposing anesthetized rats to a high ambient temperature of 42 degrees C; the moment at which the mean arterial pressure began to decrease from its peak level was taken as the onset of heatstroke. It was found that, during the heatstroke-induced cerebral ischemia and neuronal damage, the extracellular concentration of either dopamine, serotonin or norepinephrine were increased in the hypothalamus, the corpus striatum and other brain regions. In addition, the concentration of interleukin-1 (IL-1), IL-6 and tumor necrosis factor in both the plasma and brain was also increased during heatstroke-induced cerebral ischemia and neuronal damage. Heatstroke-induced cerebral ischemia and neuronal damage were attenuated by depletion of brain dopamine or serotonin produced by intracerebral injection of 6-hydroxydopamine or 5,7-dihydroxytryptamine, respectively. Accordingly, the survival of these heatstroke rats was increased after brain dopamine or serotonin depletion. Furthermore, heatstroke-induced cerebral ischemia, neuronal damage and monoamine accumulation were attenuated by blockade of IL-1 receptor produced by treatment with an IL-1 receptor antagonist. The survival of the heatstroke rats was also increased after induction of heat shock protein. The results suggest that marked accumulation of either dopamine, serotonin or IL-1 in brain is important for the occurrence of heatstroke-induced cerebral ischemia and neuronal damage in rats. The survival of these heatstroke rats can be increased by inhibition of IL-1 receptors or monoamine system in brain as well as by induction of heat shock protein.
A Bayesian Approach to Discovering Truth from Conflicting Sources for Data Integration

In practical data integration systems, it is common for the data sources being integrated to provide conflicting information about the same entity. Consequently, a major challenge for data integration is to derive the most complete and accurate integrated records from diverse and sometimes conflicting sources. We term this challenge the truth finding problem. We observe that some sources are generally more reliable than others, and therefore a good model of source quality is the key to solving the truth finding problem. In this work, we propose a probabilistic graphical model that can automatically infer true records and source quality without any supervision. In contrast to previous methods, our principled approach leverages a generative process of two types of errors (false positive and false negative) by modeling two different aspects of source quality. In so doing, ours is also the first approach designed to merge multi-valued attribute types. Our method is scalable, due to an efficient sampling-based inference algorithm that needs very few iterations in practice and enjoys linear time complexity, with an even faster incremental variant. Experiments on two real world datasets show that our new method outperforms existing state-of-the-art approaches to the truth finding problem.
Diversity and origins of Indian multi‐triazole resistant strains of Aspergillus fumigatus

Aspergillus fumigatus is a widespread opportunistic fungal pathogen causing an alarmingly high mortality rate in immunocompromised patients. Nosocomial infections by drug‐resistant A. fumigatus strains are of particular concern, and there is a pressing need to understand the origin, dispersal and long‐term evolution of drug resistance in this organism. The objective of this study was to investigate the diversity and putative origins of triazole resistance of A. fumigatus from India. Eighty‐nine isolates, including 51 multiple triazole resistant (MTR) isolates and 38 azole‐susceptible isolates, were genotyped using multilocus sequence typing (MLST), mating typing and PCR fingerprinting. MLST resolved the 51 MTR isolates into three genotypes, two of which have susceptible counterparts, suggesting that MTR isolates originated multiple times in India. The multiple‐origin hypothesis was further supported by the diversity of sequences at the triazole target gene CYP51A among the MTR isolates, and by PCR fingerprints. Interestingly, there is abundant evidence for mating and recombination in natural population of A. fumigatus in India, suggesting that sexual spread of TR34/L98H, the dominant MTR allele, is possible. Our results call for greater attention to MTR in A. fumigatus and for better management of antifungal drug use.
A Large Publicly Accassible Prototype Audio Database for Music Research

This paper introduces Codaich, a large and diverse publicly accessible database of musical recordings for use in music information retrieval (MIR) research. The issues that must be dealt with when constructing such a database are discussed, as are ways of addressing these problems. It is suggested that copyright restrictions may be overcome by allowing users to make customized feature extraction queries rather than allowing direct access to recordings themselves. The jMusicMetaManager software is introduced as a tool for improving metadata associated with recordings by automatically detecting inconsistencies and redundancies.
Diabetes and Progression of Carotid Atherosclerosis: The Insulin Resistance Atherosclerosis Study

Objective—We sought to determine the rate of progression of carotid atherosclerosis in persons with normal glucose tolerance, impaired glucose tolerance, and undiagnosed and diagnosed type 2 diabetes. Methods and Results—The Insulin Resistance Atherosclerosis Study (IRAS) is an observational cohort study in which 1192 men and women were examined at a 5-year interval. Participants of 3 ethnic groups (non-Hispanic white, African American, and Hispanic) were selected from the general population to represent a range of glucose tolerance. Baseline and follow-up ultrasound studies were obtained to estimate progression of common carotid artery (CCA) and internal carotid artery (ICA) intimal-medial thickness (IMT). Baseline glucose tolerance status was defined by an oral glucose tolerance test and World Health Organization criteria. In persons with normal glucose tolerance, progression of CCA IMT was 3.8 &mgr;m/y, and ICA IMT, 17.7 &mgr;m/y. In both CCA and ICA, progression of IMT, unadjusted for cardiovascular disease (CVD) risk factors, was approximately twice the rate in persons with diabetes than in those with normal or impaired glucose tolerance. Adjustment for CVD risk factors attenuated these differences somewhat in both sites of the carotid artery. Persons with undiagnosed diabetes had a greater ICA IMT progression rate than did persons with diagnosed diabetes (33.9 &mgr;m/y vs 26.6 &mgr;m/y, P =NS). Progression rates did not differ between persons with normal and impaired glucose tolerance. Conclusions—Progression of carotid atherosclerosis is accelerated in persons with diabetes. Progression of ICA IMT is most pronounced in persons with undiagnosed diabetes. Early identification of diabetes and CVD risk factor control might reduce its atherosclerotic complications.
Functional Characterization of Intracellular and Secreted Forms of a Truncated Hepatitis C Virus E2 Glycoprotein

ABSTRACT The E2 protein of hepatitis C virus (HCV) is believed to be a virion surface glycoprotein that is a candidate for inclusion in an antiviral vaccine. A truncated soluble version of E2 has recently been shown to interact with CD81, suggesting that this protein may be a component of the receptor for HCV. When expressed in eukaryotic cells, a significant proportion of E2 forms misfolded aggregates. To analyze the specificity of interaction between E2 and CD81, the aggregated and monomeric forms of a truncated E2 glycoprotein (E2661) were separated by high-pressure liquid chromatography and analyzed for CD81 binding. Nonaggregated forms of E2 preferentially bound CD81 and a number of conformation-dependent monoclonal antibodies (MAbs). Furthermore, intracellular forms of E2661 were found to bind CD81 with greater affinity than the extracellular forms. Intracellular and secreted forms of E2661 were also found to differ in reactivity with MAbs and human sera, consistent with differences in antigenicity. Together, these data indicate that proper folding of E2 is important for its interaction with CD81 and that modifications of glycans can modulate this interaction. Identification of the biologically active forms of E2 will assist in the future design of vaccines to protect against HCV infection.
On the differential nature of induced and incidental echolalia in autism.

BACKGROUND Echolalia is a verbal disorder, defined as 'a meaningless repetition of the words of others'. It is pathological, automatic and non-intentional behaviour, often observed in a variety of neurological and psychiatric disorders and above all in autism. We assume that echolalia is an imitative behaviour that is due to difficulties in inhibiting automatic repetition as seen in patients with frontal lobe damage. Our aim is to study the occurrence of echolalia under experimental conditions to investigate the nature of the phenomenon and its relationship with the severity of autism. METHODS Eighteen participants with autism from 17 to 36 years old were recruited; they were administrated the Vineland scale, the Observational Rating Scale of Basic Functions and the Echolalia Questionnaire. In the Echolalia Questionnaire, questions were directly addressed to the autistic subject (induced procedure) or to the subject's caregiver while the subject was free to do what he wanted (incidental procedure). The data were analysed by multivariate regressions and Pearson's correlations. RESULTS The results showed that echolalia occurred in both experimental situations; the mean value was significantly higher in the induced procedure, but results did not support the correlation with Vineland's score in the incidental procedure. It is likely that the two situations activated different processes. In particular, echolalia was statistically higher in the induced procedure as compared with the incidental one only for subjects with low score on Vineland, but in the incidental procedure, the presence of echolalia appeared to be uninfluenced by the functional capacity of subjects. CONCLUSIONS The two experimental conditions require different monitoring systems to control this verbal behaviour. The echolalic phenomenon is an expression of dependence on the environment and may occur in a situation in which the autistic person is participating in a communicative act and, lacking inhibitory control, repeats the other's communication rather than selecting an answer. The deficit in inhibitory control in this situation does not seem to be present in subjects with higher efficiency. Incidental echolalia reflects the inability of the subject to filter out background environmental noise, which occasionally results in environmental dependency.
Gender Differences in Genetic Risk Profiles for Cardiovascular Disease

Background Cardiovascular disease (CVD) incidence, complications and burden differ markedly between women and men. Although there is variation in the distribution of lifestyle factors between the genders, they do not fully explain the differences in CVD incidence and suggest the existence of gender-specific genetic risk factors. We aimed to estimate whether the genetic risk profiles of coronary heart disease (CHD), ischemic stroke and the composite end-point of CVD differ between the genders. Methodology/Principal Findings We studied in two Finnish population cohorts, using the case-cohort design the association between common variation in 46 candidate genes and CHD, ischemic stroke, CVD, and CVD-related quantitative risk factors. We analyzed men and women jointly and also conducted genotype-gender interaction analysis. Several allelic variants conferred disease risk for men and women jointly, including rs1801020 in coagulation factor XII (HR = 1.31 (1.08–1.60) for CVD, uncorrected p = 0.006 multiplicative model). Variant rs11673407 in the fucosyltransferase 3 gene was strongly associated with waist/hip ratio (uncorrected p = 0.00005) in joint analysis. In interaction analysis we found statistical evidence of variant-gender interaction conferring risk of CHD and CVD: rs3742264 in the carboxypeptidase B2 gene, p(interaction) = 0.009 for CHD, and rs2774279 in the upstream stimulatory factor 1 gene, p(interaction) = 0.007 for CHD and CVD, showed strong association in women but not in men, while rs2069840 in interleukin 6 gene, p(interaction) = 0.004 for CVD, showed strong association in men but not in women (uncorrected p-values). Also, two variants in the selenoprotein S gene conferred risk for ischemic stroke in women, p(interaction) = 0.003 and 0.007. Importantly, we identified a larger number of gender-specific effects for women than for men. Conclusions/Significance A false discovery rate analysis suggests that we may expect half of the reported findings for combined gender analysis to be true positives, while at least third of the reported genotype-gender interaction results are true positives. The asymmetry in positive findings between the genders could imply that genetic risk loci for CVD are more readily detectable in women, while for men they are more confounded by environmental/lifestyle risk factors. The possible differences in genetic risk profiles between the genders should be addressed in more detail in genetic studies of CVD, and more focus on female CVD risk is also warranted in genome-wide association studies.
Analysis of Pig Growth from Birth to Sixty Days of Age1

Abstract Alternative versions of common nonlinear growth functions were evaluated on 433 pigs (220 gilts and 213 barrows) from birth to 61 d of age. Pigs were weighed at birth, weaning (19 d of age; SD = 2.4 d), 19 d postweaning, and 42 d postweaning. The model with the best fit based on residual standard derivation (RSD) was BW = exp [(b 0 + b 1 (age + 35) + b 2 (age + 35) 2 )], which fit each individual pig’s BW data to the function. Although the function resulted in the smallest RSD (0.336 kg), it did not predict birth BW (R = 0.65) as precisely as it predicted weaning BW and later BW (R = 0.96 to 099). Also, the RSD was different at the four weigh dates and ranged from 0.04 to 0.45 kg. Birth BW had a linear-quadratic relationship with subsequent BW. Increasing birth BW of pigs with lighter birth BW had a much greater impact on increasing subsequent BW than increasing birth BW of the heaviest pigs. Also, BW taken at 19 and 42 d postweaning had linear-quadratic relationships with weaning BW. The linear-quadratic relationships between the actual BW were predicted by fitting the exponential function to each pig’s BW data. The relationships amongst the b 0 , b 1 , and b 2 values of the pigs were nonlinear and complex. The results indicate that increasing the BW of the lightest birth BW pigs could increase the mean and decrease the variance in BW at subsequent ages.
The genome sequence of the ground tit Pseudopodoces humilis provides insights into its adaptation to high altitude

Qingle Cai (caiql@genomics.cn) Xiaoju Qian (qianxiaoju@genomics.cn) Yongshan Lang (langyongshan@genomics.cn) Yadan Luo (luoyadan@genomics.cn) Shengkai Pan (panshengkai@genomics.cn) Yuanyuan Hui (huiyuanyuan@genomics.cn) Caiyun Gou (goucy@genomics.cn) Yue Cai (caiyue@genomics.cn) Meirong Hao (haomeirong@genomics.cn) Jinyang Zhao (zhaojinyang@genomics.cn) Songbo Wang (wangsongbo@genomics.cn) Zhaobao Wang (wangzhaobao@genomics.cn) Xinming Zhang (zhangxinming@genomics.cn) Jinchao Liu (liujinchao@bgitechsolutions.com) Longhai Luo (luolh@bgitechsolutions.com) Yingrui Li (liyr@genomics.cn) Jun Wang (wangj@genomics.cn) Rongjun He (herongjun@genomics.cn) Fumin Lei (leifm@ioz.ac.cn) Jiaohui Xu (xujh@genomics.cn)
The Nature of Cyberbullying in Swedish Schools: Processes, Feelings of Remorse by Bullies, Impact on Victims and Age - and Gender Differences

Four studies were conducted to examine the nature of cyberbullying in Swedish schools using both qualitative and quantitative methods. The first two studies investigated what reasons/issues may be involved in the negative feelings that a victim of bullying may feel and how these related to different types of bullying. The content analysis yielded seven themes: helplessness, persistency, fright, anonymity, no avoidance, embarrassment and loneliness. Study Three used quantitative methods to examine various issues such as gender and age differences, but especially the distribution of the bullying material, the role of bystanders, and whether cyberbullies feel more or less remorse compared to traditional bullies. Findings showed that cyberbullies not only targeted their victims, but quite often showed the material to other people and/or uploaded it onto the Internet. The bystanders of cyberbullying mostly did nothing further to distribute the material, however when they did, they tended to help the victim more often than bully him/her further. When asked about feelings of remorse, cyberbullies expressed less remorse than traditional bullies. The findings are discussed in relation to the definition of bullying, and the need for empathy raising awareness for bullies within the cyberbullying context. Study Four, a qualitative study, involved 10 pupils and examined issues such as what the pupils had experienced (as victims, bullies or bystanders), how it felt (impact), and how it was resolved. Practical implications of the findings include the highlighted need for different coping strategies to be applied for victims of cyberbullying and traditional bullying, as well as starting preventive strategies for cyberbullying in pupils as young as 7 years. In addition, the need to investigate cyberbullying in a different manner than that of traditional bullying is raised. This could have practical implications for researchers, but is also a theoretical concern related to the definition of cyberbullying.
Rational components of Hilbert schemes

The Gr\"obner stratum of a monomial ideal $\id{j}$ is an affine variety that parametrizes the family of all ideals having $\id{j}$ as initial ideal (with respect to a fixed term ordering). The Gr\"obner strata can be equipped in a natural way of a structure of homogeneous variety and are in a close connection with Hilbert schemes of subvarieties in the projective space $\PP^n$. Using properties of the Gr\"obner strata we prove some sufficient conditions for the rationality of components of $\hilb_{p(z)}^n$. We show for instance that all the smooth, irreducible components in $\hilb_{p(z)}^n$ (or in its support) and the Reeves and Stillman component $H_{RS}$ are rational.