Miracle-dz/UniFAR-FTUs huggingface dataset:
Behavioral outcomes and evidence of psychopathology among very-low-birth-weight infants at age 20 years

What reports are available indicate that very-low-birth-weight (VLBW) infants weighing less than 1.5 kg at birth experience neurodevelopmental sequelae and perform poor educationally, effects that continue into the adult years. As part of a longitudinal study, the investigators assessed behavioral outcomes and psychopathology in a cohort of 241 former VLBW infants who survived and were reevaluated at age 20 years. The infants, born from 1977 to 1979, had a mean birth weight of 1180 g and a mean gestational age at birth of 29.7 weeks. The 116 men and 125 women were matched with 233 control subjects of normal birth weight. Evaluative instruments included the Achenbach Young Adult Self-Report, the Young Adult Behavior Checklist for parents, and the ADHD (attention-deficit/hyperactivity disorder) Rating Scale for Adults, the latter completed by both young adults and their parents. Gender-specific outcomes were adjusted for sociodemographic status. VLBW men reported significantly fewer delinquent behaviors than the normal-birth-weight (NBW) control men, but there were no differences in total problem behaviors or in internalizing or eternalizing behavior problems. The parents of VLBW men reported significantly more thought problems in their sons than did control parents. VLBW women reported significantly more withdrawn behaviors but fewer delinquent behaviors than their controls. Anxious/depressed and withdrawn behaviors were nearly twice as frequent in these women than in controls. Parents of VLBW women reported significantly higher scores on the anxious/depressed, withdrawn, and attention problem subscales than did control parents. No differences were apparent in young adult self-reports of ADHD. Parents of VLBW men reported higher scores for the attentional aspect of ADHD but not higher rates of ADHD itself. These findings point toward significantly more psychopa hology in young adults who formerly were VLBW infants than in control subjects. Awareness of these problems will permit anticipatory guidance and early intervention.
Chemical profiling of bioactive constituents in hop cones and pellets extracts by online comprehensive two-dimensional liquid chromatography with tandem mass spectrometry and direct infusion Fourier transform ion cyclotron resonance mass spectrometry.

Humulus lupulus L. (hop) is highly interesting from a nutraceutical perspective. The hop phytocomplex contains a wide range of bioactive metabolites, and its characterization is challenging. To tackle such a task, for the first time we applied and compared a combined approach consisting of online comprehensive two-dimensional liquid chromatography with tandem mass spectrometry and direct infusion Fourier transform ion cyclotron mass spectrometry. A reversed phase × reversed phase approach with a shifted gradient in the second dimension ensured selectivity and two-dimensional space coverage. Hyphenation with an ion trap time-of-flight analyzer led to the identification of 83 compounds in 70 min, comprising a novel quercetin derivative and six unknown bitter acids. On the other hand, the direct infusion method was able to identify 40 analytes (except isomers) with high mass accuracy (≤ 0.1 ppm) in less than 1 min analysis time. The developed approach can be used in a complementary way, combining the separation capability and high informative spectra of two-dimensional liquid chromatography tandem mass spectrometry with the ultra-high mass accuracy of direct infusion, for potential compound discovery or the accurate profiling of bioactive compounds in different hop cultivars as well as for monitoring processing and storage of hop-based products.
Extraction and determination of tricyclic antidepressants in real samples using air-dispersed liquid-liquid microextraction prior to gas chromatography and flame ionization detection.

In the present research, a novel microextraction method was used based on dispersive liquid-liquid microextraction using low-density solvent for the determination of trace amounts of amitriptyline and doxepin as model compounds in human plasma and spring water samples before gas chromatography and flame ionization detection. The parameters influencing the extraction efficiencies including type of the extracting solvent, volume of the aqueous sample solution (donor phase), volume of the extraction solvent (acceptor phase), the number of air-injection, and the effects of pH and ionic strength were optimized. Under the optimized conditions, the obtained enrichment factors were >80. By plotting peak areas of the sample solutions versus various concentrations of the analytes, calibration curves were obtained which show the linear ranges of 10-3000 ng/mL with correlation coefficients of >0.996. The precision of the method was calculated <4.2 and the limit of detection was 1 ng/mL for two analytes. The proposed microextraction method was used for the extraction of the analytes in environmental water and plasma samples and the calculated relative recoveries were all >91%.
VeA and MvlA repression of the cryptic orsellinic acid gene cluster in Aspergillus nidulans involves histone 3 acetylation

A perplexing aspect of fungal secondary metabolite gene clusters is that most clusters remain ‘silent’ under common laboratory growth conditions where activation is obtained through gene manipulation or encounters with environmental signals. Few proteins have been found involved in repression of silent clusters. Through multicopy suppressor mutagenesis, we have identified a novel cluster suppressor in Aspergillus nidulans, MvlA (modulator of veA loss). Genetic assessment of MvlA mutants revealed the role of both itself and VeA (but not the VeA partner LaeA) in the suppression of the cryptic ors gene cluster producing orsellinic acid and its F9775 derivatives. Loss of veA upregulates F9775A and F9775B production and this increase is reduced 4–5‐fold when an overexpression mvlA (OE:mvlA) allele is introduced into the ΔveA background. Previous studies have implicated a positive role for GcnE (H3K9 acetyltransferase of the SAGA/ADA complex) in ors cluster expression and here we find expression of gcnE is upregulated in ΔveA and suppressed by OE:mvlA in the ΔveA background. H3K9 acetylation levels of ors cluster genes correlated with gcnE expression and F9775 production in ΔveA and OE:mvlAΔveA strains. Finally, deletion of gcnE in the ΔveA background abolishes ors cluster activation and F9775 production. Together, this work supports a role for VeA and MvlA in modifying SAGA/ADA complex activity.
A single‐molecule approach to DNA replication in Escherichia coli cells demonstrated that DNA polymerase III is a major determinant of fork speed

The replisome catalyses DNA synthesis at a DNA replication fork. The molecular behaviour of the individual replisomes, and therefore the dynamics of replication fork movements, in growing Escherichia coli cells remains unknown. DNA combing enables a single‐molecule approach to measuring the speed of replication fork progression in cells pulse‐labelled with thymidine analogues. We constructed a new thymidine‐requiring strain, eCOMB (E. coli for combing), that rapidly and sufficiently incorporates the analogues into newly synthesized DNA chains for the DNA‐combing method. In combing experiments with eCOMB, we found the speed of most replication forks in the cells to be within the narrow range of 550–750 nt s−1 and the average speed to be 653 ± 9 nt s−1 (± SEM). We also found the average speed of the replication fork to be only 264 ± 9 nt s−1 in a dnaE173‐eCOMB strain producing a mutant‐type of the replicative DNA polymerase III (Pol III) with a chain elongation rate (300 nt s−1) much lower than that of the wild‐type Pol III (900 nt s−1). This indicates that the speed of chain elongation by Pol III is a major determinant of replication fork speed in E. coli cells.
Identification of the recently described Cronobacter condimenti by an rpoB-gene-based PCR system.

Enterobacter sakazakii is an important foodborne pathogen, which can cause meningitis, necrotizing enterocolitis and bacteraemia in neonates. Updating the original taxonomy of E. sakazakii by using a polyphasic approach has resulted in the definition of six novel species (C. sakazakii, C. malonaticus, C. turicensis, C. muytjensii, C. dublinensis and Cronobacter sp. genomospecies 1) and the transfer of these species to a novel genus, Cronobacter (Iversen et al., 2007, 2008), in order to facilitate their continued inclusion in schemata for diagnosis, with the novel genus being contaxic with E. sakazakii. In a study by Stoop et al. (2009), an rpoB-genetargeted PCR assay was developed, which enables the identification of members of the genus Cronobacter to the species level. In a recent study by Joseph et al. (2012) an additional species, C. condimenti, was described within the genus Cronobacter, and a novel species designation, C. universalis, was proposed for the formerly named Cronobacter sp.genomospecies 1. However, as of yet, no species-specific identification systems are available for C. condimenti. Here, we report an extension of the rpoB-gene-based PCR system (Stoop et al., 2009) for identification of this species. The rpoB gene encodes the b-subunit of the bacterial ribosomal polymerase, which is a well-recognized polymorphic marker and is useful for the identification of bacteria. The rpoB gene sequence of C. condimenti 1330 (5CECT 7863 5LMG 26250) was deposited in GenBank (http://www.ncbi. nlm.nih.gov/genbank/) under the accession number JQ316670.
Reformulating software engineering as a search

Metaheuristic techniques such as genecc algorithms, simulated annealing and tabu search have found wide application in most areas of engineering. These techniques have also been applied in business, financial and economic modelling. Metaheuristics have been applied to three areas of software engineering: test data generation, module clustering and cost/effort prediction, yet there remain many software engineering problems which have yet to be tackled using metaheuristics. It is surprising that metaheuristics have not been more widely applied to software engineering; many problems in software engineering are characterised by precisely the features which make metaheuristics search applicable. In the paper it is argued that the features which make metaheuristics applicable for engineering and business applications outside software engineering also suggest that there is great potential for the exploitation of metaheuristics within software engineering. The paper briefly reviews the principal metahenristic search techniques and surveys existing work on the application of metaheuristics to the three software engineering areas of test data generation, module clustering and cost/effort prediction. It also shows how metaheuristic search techniques can be applied to three additional areas of software engineering: maintenance/evolution system integration and requirements scheduling. The soft- ware engineering problem areas considered thus span the range of the software development process, from initial planning, cost estimation and requirements analysis through to integration, maintenance and evolution of legacy systems. The aim is to justify the claim that many problems in software engineering can be reformulated as search problems. to which metaheuristic techniques can be applied. The goal of the paper is to stimulate greater interest in metaheuristic search as a tool of optimisation of software engineering problems and to encourage the investigation and exploitation of these technologies in finding near optimal solutions to the complex constraint-based scenarios which arise so frequently in software engineering.
Comparative study of clustering algorithms and abstract representations for software remodularisation

As valuable software systems become older, reverse engineering becomes increasingly important to companies that have to maintain the code. Clustering is a key activity in reverse engineering that is used to discover improved designs of systems or to extract significant concepts from code. Clustering is an old, highly sophisticated, activity which offers many methods to meet different needs. The various methods have been well documented in the past; however, conclusions from general clustering literature may not apply entirely to the reverse engineering domain. In the paper, the authors study three decisions that need to be made when clustering: the choice of (i) abstract descriptions of the entities to be clustered, (ii) metrics to compute coupling between the entities, and (iii) clustering algorithms. For each decision, our objective is to understand which choices are best when performing software remodularisation. The experiments were conducted on three public domain systems (gcc, Linux and Mosaic) and a real world legacy system (2 million LOC). Among other things, the authors confirm the importance of a proper description scheme for the entities being clustered, list a few effective coupling metrics and characterise the quality of different clustering algorithms. They also propose description schemes not directly based on the source code, and advocate better formal evaluation methods for the clustering results.
Discovery of a bifunctional cardiolipin/phosphatidylethanolamine synthase in bacteria

Phosphatidylethanolamine (PE) and cardiolipin (CL) are major components of bacterial and eukaryotic membranes. In bacteria, synthesis of PE usually occurs via decarboxylation of phosphatidylserine (PS) by PS decarboxylases (Psd). CL is produced by various CL synthases (Cls). Membranes of the plant pathogen Xanthomonas campestris predominantly contain PE, phosphatidylglycerol (PG) and CL. The X. campestris genome encodes one Psd and six putative CLs. Deletion of psd resulted in loss of PE and accumulation of PS. The mutant was severely affected in growth and cell size. PE synthesis, growth and cell division were partially restored when cells were supplied with ethanolamine (EA) suggesting a previously unknown PE synthase activity. Via mutagenesis, we identified a Cls enzyme (Xc_0186) responsible for EA‐dependent PE biosynthesis. Xanthomonas lacking xc_0186 not only lost its ability to utilize EA for PE synthesis but also produced less CL suggesting a bifunctional enzyme. Recombinant Xc_0186 in E. coli and in cell‐free extracts uses cytidine diphosphate diacylglycerol (CDP‐DAG) and PG for CL synthesis. It is also able to use CDP‐DAG and EA for PE synthesis. Owing to its dual function in CL and PE production, we consider Xc_0186 the founding member of a new class of enzymes called CL/PE synthase (CL/PEs).
The double triangular test in practice

The double triangular test was introduced twenty years ago, and the purpose of this paper is to review applications that have been made since then. In fact, take‐up of the method was rather slow until the late 1990s, but in recent years several clinical trial reports have been published describing its use in a wide range of therapeutic areas. The core of this paper is a detailed account of five trials that have been published since 2000 in which the method was applied to studies of pancreatic cancer, breast cancer, myocardial infarction, epilepsy and bedsores. Before those accounts are given, the method is described and the history behind its evolution is presented. The future potential of the method for sequential case–control and equivalence trials is also discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Reliability of the EK Scale, a Functional Test for Non-ambulatory Persons with Duchenne Dystrophy

The EK {Egen Klassifikation} scale was developed to assess overall functional ability in the non-ambulatory stage of Duchenne muscular dystrophy (DMD). The purpose of this study was to examine the reliability of the EK scale. Six subjects with DMD, selected as representative of the entire range of functional ability seen in the nonambulatory phase of the disease, were video recorded and assessed using the EK scale. The assessment required both interview and performance of functional activities. The video records were shown to 17 healthcare professionals comprising seven three physiotherapy students, four occupational therapists, two social workers and one physician. They viewed and assessed the video recordings. Seven of the professionals repeated the assessments after 6-8 weeks. Intra-class correlation coefficients determined for both inter- and intra-rater reliability were 0.98. The standard deviation of individual estimates of EK sum was 0.95 when physiotherapists, an assessment was repeated by different evaluators on the same subject and 0.78 when repeated by the same evaluator. Weighted kappa values for individual categories ranged from 0.67 to 0.94. The EK scale was found to be highly reliable when used by healthcare professionals assessing the subjects from videotapes.
Utilization of host‐derived cysteine‐containing peptides overcomes the restricted sulphur metabolism of Campylobacter jejuni

The non‐glycolytic food‐borne pathogen Campylobacter jejuni successfully colonizes the intestine of various hosts in spite of its restricted metabolic properties. While several amino acids are known to be used by C. jejuni as energy sources, none of these have been found to be essential for growth. Here we demonstrated through phenotype microarray analysis that cysteine utilization increases the metabolic activity of C. jejuni. Furthermore, cysteine was crucial for its growth as C. jejuni was unable to synthesize it from sulphate or methionine. Our study showed that C. jejuni compensates this limited anabolic capacity by utilizing sulphide, thiosulphate, glutathione and the dipeptides γGlu–Cys, Cys–Gly and Gly–Cys as sulphur sources and cysteine precursors. A panel of C. jejuni mutants in putative peptidases and peptide transporters were generated and tested for their participation in the catabolism of the cysteine‐containing peptides, and the predicted transporter protein CJJ81176_0236 was discovered to facilitate the growth with the dipeptide Cys–Gly, Ile–Arg and Ile–Trp. It was named Campylobacter peptide transporter A (CptA) and is the first representative of the oligopeptide transporter OPT family demonstrated to participate in the glutathione‐derivative Cys–Gly catabolism in prokaryotes. Our study provides new insights into how host‐ and microbiota‐derived substrates like sulphide, thiosulphate and short peptides are used by C. jejuni to compensate its restricted metabolic capacities.
Pbp2x localizes separately from Pbp2b and other peptidoglycan synthesis proteins during later stages of cell division of Streptococcus pneumoniae D39

The relative localization patterns of class B penicillin‐binding proteins Pbp2x and Pbp2b were used as positional indicators of septal and peripheral (side‐wall‐like) peptidoglycan (PG) synthesis, respectively, in the mid‐cell regions of Streptococcus pneumoniae cells at different stages of division. We confirm that Pbp2x and Pbp2b are essential in the strain D39 genetic background, which differs from that of laboratory strains. We show that Pbp2b, like Pbp2x and class A Pbp1a, follows a different localization pattern than FtsZ and remains at division septa after FtsZ reappears at the equators of daughter cells. Pulse‐experiments with fluorescent D‐amino acids (FDAAs) were performed in wild‐type cells and in cells in which Pbp2x activity was preferentially inhibited by methicillin or Pbp2x amount was depleted. These experiments show that Pbp2x activity separates from that of other PBPs to the centres of constricting septa in mid‐to‐late divisional cells resolved by high‐resolution 3D‐SIM microscopy. Dual‐protein and protein‐fluorescent vancomycin 2D and 3D‐SIM immunofluorescence microscopy (IFM) of cells at different division stages corroborate that Pbp2x separates to the centres of septa surrounded by an adjacent constricting ring containing Pbp2b, Pbp1a and regulators, StkP and MreC. The separate localization of Pbp2x suggests distinctive roles in completing septal PG synthesis and remodelling.
The redundant aminotransferases in lysine and arginine synthesis and the extent of aminotransferase redundancy in Escherichia coli

Aminotransferases can be redundant or promiscuous, but the extent and significance of these properties is not known in any organism, even in Escherichia coli. To determine the extent of redundancy, it was first necessary to identify the redundant aminotransferases in arginine and lysine synthesis, and then complement all aminotransferase‐deficient mutants with genes for all aminotransferases. The enzymes with N‐acetylornithine aminotransferase (ACOAT) activity in arginine synthesis were ArgD, AstC, GabT and PuuE; the major anaerobic ACOAT was ArgD. The major enzymes with N‐succinyl‐l,l‐diaminopimelate aminotransferase (SDAP‐AT) activity in lysine synthesis were ArgD, AstC, and SerC. Seven other aminotransferases, when overproduced, complemented the defect in a triple mutant. Lysine availability did not regulate synthesis of the major SDAP‐ATs. Complementation analysis of mutants lacking aminotransferases showed that the SDAP‐ATs and alanine aminotransferases were exceptionally redundant, and it is proposed that this redundancy may ensure peptidoglycan synthesis. An overview of all aminotransferase reactions indicates that redundancy and broad specificity are common properties of aminotransferases.
Encouraging legal help seeking for victims of intimate partner violence: the therapeutic effects of the civil protection order.

Civil protective orders (CPOs) are the most widely used justice system remedy for intimate partner violence (IPV), and were implemented to ensure safety and increase victim participation in the justice system. Limited data exists regarding the effectiveness of CPOs; however, theories of therapeutic jurisprudence argue that legal interventions in and of themselves can improve mental health outcomes. To test this hypothesis, we examined the effectiveness of having a CPO issued against one's abuser at improving the psychological sequelae of exposure to trauma. We used a longitudinal sample of female residents of battered women's shelters who had experienced IPV (N = 106; 55% African American). One-way analyses of variance using gain scores indicated that PTSD symptoms (effect size η(p)(2) = . 16) and incidents of sexual revictimization (effect size η(p)(2) = . 09) decreased from baseline to 6-months postshelter for women who had a CPO against their most recent abuser compared to women without a CPO. These results support theories of therapeutic jurisprudence, suggesting that having a CPO can improve mental health outcomes. Limitations and clinical implications of our findings are discussed, including arguing for a coordinated service system that incorporates both legal and psychological assistance to improve the mental health of victims of IPV.
Advice complexity of disjoint path allocation

This paper contributes to the research of advice complexity of online problems. Namely, we discuss the disjoint path allocation problem in various versions, based on the choice of values of the calls, and ability to preempt. The advice complexity is measured relative to either the length of the input sequence of requests, or the length of the input path. We provide lower and upper bounds on advice complexity of optimal online algorithms for these problems, and some bounds on trade-off between competitiveness and advice complexity. One of the results is an improved lower bound of n − 1 on advice complexity for the non-preemptive version with constant values of calls. For all considered variations, the newly provided lower and upper bounds on advice complexity of optimal algorithms are linear, and therefore asymptotically tight.