Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication Forks Stalled at Ultraviolet Lesions Are Rescued via RecA and RuvABC Protein-catalyzed Disintegration in Escherichia coli*

Background: Ultraviolet (UV) light causes genetic instability, suggesting chromosome fragmentation. Results: UV light induces chromosomal fragmentation, which is independent of excision of UV lesions but requires replication forks, homologous strand exchange, and Holliday junction resolution. Conclusion: Fragmentation is a result of replication fork reversal and breakage. Significance: Breakage is the first step in rescuing stalled replication forks. Ultraviolet (UV) irradiation is not known to induce chromosomal fragmentation in sublethal doses, and yet UV irradiation causes genetic instability and cancer, suggesting that chromosomes are fragmented. Here we show that UV irradiation induces fragmentation in sublethal doses, but the broken chromosomes are repaired or degraded by RecBCD; therefore, to observe full fragmentation, RecBCD enzyme needs to be inactivated. Using quantitative pulsed field gel electrophoresis and sensitive DNA synthesis measurements, we investigated the mechanisms of UV radiation-induced chromosomal fragmentation in recBC mutants, comparing five existing models of DNA damage-induced fragmentation. We found that fragmentation depends on active DNA synthesis before, but not after, UV irradiation. At low UV irradiation doses, fragmentation does not need excision repair or daughter strand gap repair. Fragmentation absolutely depends on both RecA-catalyzed homologous strand exchange and RuvABC-catalyzed Holliday junction resolution. Thus, chromosomes fragment when replication forks stall at UV lesions and regress, generating Holliday junctions. Remarkably, cells specifically utilize fork breakage to rescue stalled replication and avoid lethality.
ICF syndrome in a girl with DNA hypomethylation but without detectable DNMT3B mutation

A 3‐year‐old girl with phenotypic and cytogenetic manifestations of the ICF syndrome and DNA hypomethylation but without DNMT3B gene mutation is described. At age 3 months, she had an apneic spell that left her with spastic paraplegia and severe mental retardation. At age 8 months, she suffered meningococcal meningitis and sepsis. When seen by us at age 3 years with virilization, she had a cleft plate, macroglossia, and an atrial septal defect. An adenoma was surgically removed from the right adrenal cortex. Her serum immunoglobulin levels were normal except IgA at the low normal border. Her lymphocytes showed paracentromeric stretching of chromosomes 1 and 16 in 7% of metaphases, and multiradial figures involving these chromosomes in 1% of cells. Hypomethylation of classical satellite 2 DNA was observed with BstBI digestion, but in a lesser degree than those in the individuals with proven DNMT3B mutations. No mutation was found in the coding and promoter regions of the gene. Several alternative interpretations were considered to explain the low frequencies of chromosomal instabilities and the lower degree of DNA hypomethylation, and undetected DNA3B mutations. A mutation may be present in the gene but undetected, present in other DNA methyltransferases (DNMT) genes or in a DNMT‐associated protein gene. © 2004 Wiley‐Liss, Inc.
Mevalonate and Nonmevalonate Pathways for the Biosynthesis of Isoprene Units

Isoprenoids are synthesized by consecutive condensations of their five-carbon precursor, isopentenyl diphosphate, to its isomer, dimethylallyl diphosphate. Two pathways for these precursors are known. One is the mevalonate pathway, which operates in eucaryotes, archaebacteria, and cytosols of higher plants. The other is a recently discovered pathway, the nonmevalonate pathway, which is used by many eubacteria, green algae, and chloroplasts of higher plants. To date, five reaction steps in this new pathway and their corresponding enzymes have been identified. EC numbers of these enzymes have been assigned by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and are available at http://www.chem.qmw.ac. uk/iubmb/enzyme/reaction/terp/nonMVA.html.
The essential Escherichia coli msgB gene, a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpE, is identical to dapE

The grpE gene product is one of three Escherichia coli heat shock proteins (DnaK, DnaJ, and GrpE) that are essential for both bacteriophage lambda DNA replication and bacterial growth at all temperatures. In an effort to determine the role of GrpE and to identify other factors that it may interact with, we isolated multicopy suppressors of the grpE280 point mutation, as judged by their ability to reverse the temperature-sensitive phenotype of grpE280. Here we report the characterization of one of them, designated msgB. The msgB gene maps at approximately 53 min on the E. coli chromosome. The minimal gene possesses an open reading frame that encodes a protein with a predicted size of 41,269 M(r). This open reading frame was confirmed the correct one by direct amino-terminal sequence analysis of the overproduced msgB gene product. Genetic experiments demonstrated that msgB is essential for E. coli growth in the temperature range of 22 to 37 degrees C. Through a sequence homology search, MsgB was shown to be identical to N-succinyl-L-diaminopimelic acid desuccinylase (the dapE gene product), which participates in the diaminopimelic acid-lysine pathway involved in cell wall biosynthesis. Consistent with this finding, the msgB null allele mutant is viable only when the growth medium is supplemented with diaminopimelic acid. These results suggest that GrpE may have a previously unsuspected function(s) in cell wall biosynthesis in E. coli.
Real-time fNIRS signal acquisition system: Compatible with TMS

Functional near-infrared spectroscopy (fNIRS) is a non-invasive neural imaging tool which provides information of the oxidative metabolism in the brain by using diffused near-infrared light. Transcranial magnetic stimulation (TMS) is a physical stimulus, which can directly interfere with the neuron activity. The combination of fNIRS with TMS enables researchers to directly study the dynamic causality between different brain regions and the network of the particular brain region. In this paper, we design a dual channels real-time fNIRS system that can work during TMS stimulus. This system consists of hardware part and software part, to realize the blood oxygen signal acquisition and analog-to-digital conversion. The hardware part includes optical fiber probe and acquisition card of the national instruments. Software part is based on the LabVIEW, to develop the PC software, to implement the control of the system and the real-time display and storage of signals.
Mechanisms of Platelet-Neutrophil Interactions and Effects on Cell Filtration in Septic Shock

We examined the mechanisms and the adhesive molecules mediating platelet-neutrophil adhesion in patients with septic shock. Neutrophils, platelets, and platelet poor plasma (NPPP) were isolated from 12 normal volunteers. Platelets and neutrophils were stimulated with platelet poor plasma (SPPP) removed from 12 patients in septic shock. Cell adhesion was assessed by filtration through 5-&mgr;m pore filters and by flow cytometry. Blocking monoclonal antibodies were used against the platelet and neutrophil surface receptors glycoprotein complex IIb/IIIa, P-selectin, ICAM-2, CD11a, CD11b, and CD18. The filtration pressure (Pi) of cells suspended in SPPP was significantly greater than that of cells suspended in NPPP (24 ± 1.0 mmHg vs. 14 ± 1.0 mmHg;P < 0.05). The difference between the Pi of cells suspended in SPPP or NPPP (&Dgr;Pi SPPP-NPPP) in the presence of monoclonal antibodies anti-CD41, anti-CD62P, abciximab, anti-CD11a, anti-CD11b, and anti-CD18 was significantly less than the &Dgr;Pi SPPP-NPPP of cell suspensions without the addition of these monoclonal antibodies (P < 0.01). The greatest reduction in Pi occurred when platelet receptor P-selectin was blocked simultaneously with the CD11b receptor on the neutrophil as compared to all other single blocking monoclonal antibodies or combinations of monoclonal antibodies. The mean fluorescence of activated platelet CD63-PE binding to neutrophils suspended in SPPP was significantly greater than that of cells suspended in NPPP (780 ± 130 lfu vs. 295 ± 35 lfu;P < 0.05). The greatest attenuation in mean fluorescence occurred by blocking the P-selectin receptor on the platelet simultaneously with CD11b receptor on the neutrophil. We conclude that platelet-neutrophil aggregation is increased in septic shock. This aggregation is mediated by the interaction of multiple platelet and neutrophil surface receptors. The platelet receptor P-selectin and the neutrophil receptor CD11b/CD18 appear to play the most important role in these interactions.
Sample preparation project for the subcellular proteome of mouse liver

Organelle proteome has become one of the most important fields of proteomics, and the subcellular fractionation with high purity and yield has always been a challenge for cell biologists and also for the Human Liver Proteome Project (HLPP). The liver of a C57BL/6J mouse was chosen as the model to find the optimum method for subcellular preparation. The method we selected could obtain the multiple fractions including plasma membrane, mitochondria, nucleus, ER, and cytosol from a single homogenate. With the same procedure, it is for the first time that the preparation method of frozen homogenized livers was compared with that of the fresh livers and frozen livers. We systematically evaluated the purity, efficiency, and integrity by protein yield, immunoblotting, and transmission electron microscopy. Taken together, the method of multiple fractions from a single tissue is effective enough for subcellular fractionation of mouse liver. We give a selective sample preparation method for frozen homogenized livers, for rare clinical samples, which cannot easily be used for subcellular separation immediately. But the frozen livers are not recommended for organelles isolation. This result is especially useful for sample preparation of human liver for subcellular fractionation of HLPP.
Effect of steroids on energy expenditure and substrate oxidation in women with crohn's disease

OBJECTIVE:Patients with Crohn's disease (CD) have increased energy expenditure and fat oxidation. Steroids, commonly used to treat flare-up of CD, induce weight gain. This study was designed to evaluate the effects of prednisone and budesonide on energy expenditure and substrate oxidation in patients with CD.METHODS:Twenty-nine women with CD and 10 healthy controls were studied. Ten patients received prednisone (0.75–1.0 mg/kg/day), nine received budesonide (9 mg/day), and 10 did not receive steroids. Resting energy expenditure and substrate oxidation were measured by indirect calorimetry in a fasting state and after a standard diet.METHODS:In the fasting state, resting energy expenditure was higher in patients without steroids than in the controls. Lipid oxidation was lower (p < 0.01) in patients with prednisone (0.46 ± 0.39 mg/kg/min) than in patients with budesonide (0.97 ± 0.28 mg/kg/min) and without steroids (1.06 ± 0.32 mg/kg/min), but was similar with control subjects (0.47 ± 0.20 mg/kg/min). Postprandially, lipid oxidation was lower (p < 0.01) in patients with prednisone (0.32 ± 0.23 mg/kg/min) than in patients with budesonide (0.75 ± 0.20 mg/kg/min), without steroids (0.82 ± 0.23 mg/kg/min), and controls (0.58 ± 0.15 mg/kg/min). Protein oxidation was significantly higher in patients with prednisone than in the other subjects.CONCLUSION:In women with CD, prednisone decreases lipid oxidation and increases protein oxidation. These effects are not observed with budesonide and may contribute to the weight gain and side effects commonly observed with prednisone. A low-fat/high-protein diet could be proposed during a course of prednisone.
Serum 3,3',5'-triiodothyronine (rT3) and 3,5,3'-triiodothyronine/rT3 are prognostic markers in critically ill patients and are associated with postmortem tissue deiodinase activities.

INTRODUCTION AND METHODS Critical illness is associated with reduced TSH and thyroid hormone secretion, and with changes in peripheral thyroid hormone metabolism, resulting in low serum T3 and high rT3. In 451 critically ill patients who received intensive care for more than 5 d, serum thyroid parameters were determined on d 1, 5, 15, and last day (LD). All patients had been randomized for intensive or conventional insulin treatment. Seventy-one patients died, and postmortem liver and skeletal muscle biopsies were obtained from 50 of them for analysis of deiodinase (D1-3) activities. RESULTS Insulin treatment did not affect thyroid parameters. On d 1, rT3 was higher and T3/rT3 was lower in nonsurvivors as compared with survivors (P = 0.001). Odds ratio for survival of the highest vs. the lowest quartile was 0.3 for rT3 and 2.9 for T3/rT3. TSH, T4, and T3 were lower in nonsurvivors from d 5 until LD (P < 0.001). TSH, T4, T3, and T3/rT3 increased over time in survivors, but decreased or remained unaltered in nonsurvivors. Liver D1 activity was positively correlated with LD serum T3/rT3 (R = 0.83, P < 0.001) and negatively correlated with rT3 (R = -0.69, P < 0.001). Both liver and skeletal muscle D3 activity were positively correlated with LD serum rT3 (R = 0.32, P = 0.02 and R = 0.31, P = 0.03). CONCLUSION In critically ill patients who required more than 5 d of intensive care, rT3 and T3/rT3 were already prognostic for survival on d 1. On d 5, T4, T3, but also TSH levels are higher in patients who will survive. Serum rT3 and T3/rT3 were correlated with postmortem tissue deiodinase activities.
Interactive effects of parental age on offspring fitness and age‐assortative mating in a wild bird

Abstract Variation in parental age can have important consequences for offspring fitness and the structure of populations and disease transmission. However, our understanding of the effects of parental age on offspring in natural populations is limited. Here, we investigate consequences of parental age for offspring fitness and test for age‐assortative mating in a short‐lived bird, the house wren (Troglodytes aedon). Offspring immunoresponsiveness increased with maternal age and decreased with paternal age, but the strength of these effects varied with the age of one's mate. Offspring immunoresponsiveness was augmented most with older mothers and younger fathers. Thus, we expected this combination of ages to yield the highest offspring fitness. However, offspring recruitment, longevity, and lifetime reproductive success were greatest when both parents were of above‐average age. Consistent with the interactive effects of parental age on offspring fitness, we detected positive age‐assortative mating among breeding pairs. Our results suggest that selection favors age‐assortative mating, but in different ways depending on how parental ages affect offspring. We suggest that, in this short‐lived species, selection for combinations of parental ages that maximize offspring immune responses is likely weaker than selection to produce breeding adults. GRAPHICAL ABSTRACT Offspring immune responsiveness is greatest when offspring have an older mother and a younger father, but recruitment, longevity, and lifetime reproduction are greatest when both parents are of above‐average age. Consistent with these effects, we detected positive age‐assortative mating among breeding pairs. Figure. No caption available.
Patients’ Views on Asthma-Specific Quality of Life Questionnaires: Qualitative Interview Study in Germany

Objective. It is unclear which of the commonly used asthma-specific quality of life (QoL) questionnaires best capture the lived experience of people with asthma. The objective of this study was to explore patients’ views on three asthma-specific QoL questionnaires. Methods. Ten adult individuals with asthma were asked to complete three asthma-specific QoL questionnaires (Standardized Juniper Asthma Quality of Life Questionnaire (AQLQ-J-s), Sydney Asthma Quality of Life Questionnaire (AQLQ-S), and Fragebogen zur Lebensqualität bei Asthma (FLA)). Interviews were conducted to elicit patients’ views on the questionnaires. Interviews were transcribed verbatim and thematic content analysis was performed. Results. Participants spoke about response format and options, missing and redundant/similar content as well as content that was perceived to be irrelevant. A lack of specificity was named for some items, and issues concerning layout were raised. Despite the diversity of views expressed, participants mostly agreed on the ranking of the questionnaires and, overall, favored the AQLQ-S. Conclusions. Patient involvement highlights shortcomings and strengths of various asthma-specific questionnaires in terms of both format and content. The AQLQ-S was the most positively perceived questionnaire. Future research will need to explore other settings and potentially involve a larger and more diverse sample.
Optimizing robustness in geometric routing via embedding redundancy and regeneration

Geometric routing is an alternative to traditional routing algorithms in which traffic is no longer forwarded using lookup tables, but using coordinates in an embedding of the underlying network. A major downside of current geometric routing algorithms is their inability to handle network failures in a graceful manner. Moreover, they cannot deal with dynamic graph topologies. This article presents a geometric routing scheme that uses an embedding based on a spanning forest. Allowing nodes to select the optimal spanning tree leads to both shorter paths and natural traffic redirection in case of network failures. By constructing the forest in such a way that its disconnected components have low redundancy, their coverage is maximized. Results show that this system is able to operate gracefully in severe failure scenarios, without any form of path protection or restoration. By means of an embedding regeneration procedure, the routing scheme is able to continuously adapt to an altering network topology. This geometric routing algorithm effectively combines two key objectives, namely low path stretch and high robustness. © 2015 Wiley Periodicals, Inc. NETWORKS, Vol. 66(4), 320–334 2015
Addressing Domestic Violence Through Maternal–Child Health Home Visiting: What We Do and Do Not Know

Domestic violence (DV) has been described as a public health epidemic. Health care providers of all disciplines encounter victims of DV in every practice setting. However, the vast majority of DV health care research has focused on care provided to victims in traditional acute care and clinic settings. Few investigators have conducted studies with community health nurses (CHNs) who visit DV victims in their homes. CHNs, providing preventive maternal–child health (MCH) care through home visits with families, have been described by some as key providers in DV prevention. However, there is a dearth of knowledge about the actual practice and related outcomes of these nurses when working with families experiencing DV. The purpose of this article is to provide a baseline view of the current state of knowledge on which nurses may begin building future research that leads to evidence-based practice. The article describes the potential role of home-visiting MCH nurses in DV prevention and intervention, provides a critical review of the existing research, identifies primary gaps in scientific knowledge, proposes future research priorities, and makes recommendations for practice.
Microsatellite and single‐nucleotide polymorphisms indicate recurrent transitions to asexuality in a microsporidian parasite

Assessing the mode of reproduction of microparasites remains a difficult task because direct evidence for sexual processes is often absent and the biological covariates of sex and asex are poorly known. Species with geographically divergent modes of reproduction offer the possibility to explore some of these covariates, for example, the influence of life‐history traits, mode of transmission and life‐cycle complexity. Here, we present a phylogeographical study of a microsporidian parasite, which allows us to relate population genetic structure and mode of reproduction to its geographically diverged life histories. We show that in microsporidians from the genus Hamiltosporidium, that use the cladoceran Daphnia as host, an epidemic population structure has evolved, most probably since the last Ice Age. We partially sequenced three housekeeping genes (alpha tubulin, beta tubulin and hsp70) and genotyped seven microsatellite loci in 51 Hamiltosporidium isolates sampled within Europe and the Middle East. We found two phylogenetically related asexual parasite lines, one each from Fennoscandia and Israel, which share the unique ability of being transmitted both vertically and horizontally from Daphnia to Daphnia. The sexual forms cannot transmit horizontally among Daphnia, but presumably have a complex life cycle with a second host species. In spite of the similarities between the two asexual lineages, a clustering analysis based on microsatellite polymorphisms shows that asexual Fennoscandian parasites do not share ancestry with any other Hamiltosporidium that we have sampled. Moreover, allele sequence divergence at the hsp70 locus is twice as large in Fennoscandian than in Israeli parasites. Our results indicate that asexual reproduction evolved twice independently, first in Fennoscandian and more recently in the Israeli parasites. We conclude that the independent origin of asexuality in these two populations is associated with the altered parasite mode of transmission and the underlying dynamics of host populations.
Benchmarking protein–protein interface predictions: Why you should care about protein size

A number of predictive methods have been developed to predict protein–protein binding sites. Each new method is traditionally benchmarked using sets of protein structures of various sizes, and global statistics are used to assess the quality of the prediction. Little attention has been paid to the potential bias due to protein size on these statistics. Indeed, small proteins involve proportionally more residues at interfaces than large ones. If a predictive method is biased toward small proteins, this can lead to an over‐estimation of its performance. Here, we investigate the bias due to the size effect when benchmarking protein‐protein interface prediction on the widely used docking benchmark 4.0. First, we simulate random scores that favor small proteins over large ones. Instead of the 0.5 AUC (Area Under the Curve) value expected by chance, these biased scores result in an AUC equal to 0.6 using hypergeometric distributions, and up to 0.65 using constant scores. We then use real prediction results to illustrate how to detect the size bias by shuffling, and subsequently correct it using a simple conversion of the scores into normalized ranks. In addition, we investigate the scores produced by eight published methods and show that they are all affected by the size effect, which can change their relative ranking. The size effect also has an impact on linear combination scores by modifying the relative contributions of each method. In the future, systematic corrections should be applied when benchmarking predictive methods using data sets with mixed protein sizes. Proteins 2014; 82:1444–1452. © 2014 Wiley Periodicals, Inc.