Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective enrichment of damaged DNA molecules for ancient genome sequencing

Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA—the presence of deoxyuracils—for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the fraction of useful sequence information increases ∼10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches. Furthermore, we show that U selection can lead to a four- to fivefold increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants in some samples. U selection may thus help to lower the costs for ancient genome sequencing of nonhuman samples also.
The declining influence of class and ideology in union membership: Consistent but divergent trends among Swedish employees

Using individual-level time-series data covering the period from 1990 to 2011, this article provides an empirical analysis of how the influence of various aspects of class and ideology on union organization have changed over time in the Swedish context. The primary results indicate that although union density and the influence of class-related aspects and ideology are decreasing, particularly among groups with traditionally high levels of organization, the general trend is not valid for all categories of employees. Rather, it appears that where the tradition of being organized is weaker, the influence of class and class identity is particularly strong. No evidence is identified that supports the thesis of class loyalty vanishing among the young.
Redefining Smoking and the Self as a Nonsmoker

A grounded theory approach was used to develop a substantive theory answering the question, What are older adults'experiences who have quit smoking? Interviews were conducted with 21 elders with a mean age of 67 years who had quit smoking for a minimum of 3 months and a maximum of S years. Data analysis yielded a core variable redefining smoking and the self as a nonsmoker, which was indicated by the major theoretical categories of recognizing the need to quit, making the decision, learning to be a nonsmoker, and sustaining as a nonsmoker Participants actually changed their views about smoking and themselves as smokers. They believed that they were vulnerable because of their ages and that age and smoking were a problematic combination. Findings support thatnurses and otherhealth care providers can assist olderadults in the process of quitting smoking.
Urban Parks: Volunteers and Civic Engagement

ParkScan – San Francisco, California ParkScan is a partnership of the San Francisco Recreation and Park Department and the Neighborhood Parks Council, an advocacy group. Trained observers track park and playground maintenance issues in San Francisco and in the surrounding county and use a Webbased reporting system. Maintenance conditions are made public and can be tracked at www.parkscansf. org/parkscan.aspx.
Stabilizing Technique for AC–DC Boost PFC Converter Based on Time Delay Feedback

It is well known that the ac-dc power factor correction (PFC) boost preregulator can present instability at the line frequency. This nonlinear phenomenon can jeopardize the system performances by increasing the total harmonic distortion and decreasing the power factor. In this brief, a new stabilizing technique is applied using time delay feedback when the system exhibits slow-scale instability under a traditional controller. First, the technique is applied to the averaged model. The results are then validated by numerical simulations using power simulator package. An analytical expression for the stability domain is also provided. It is proven that the proposed technique introduces many advantages to the most and widely used average current mode control through widening the stability region of the PFC converter. Moreover, this technique can also bring the same advantages to other existing commercial control methods for boost and other PFC topologies.
High Incidence of Sudden Death with Conduction System and Myocardial Disease Due to Lamins A and C Gene Mutation

BÉCANE, H. –M. , et al.: High Incidence of Sudden Death with Conduction System and Myocardial Disease Due to Lamins A and C Gene Mutation. We studied 54 living relatives from a large French kindred, among which 17 members presented with a cardiomyopathy transmitted on an autosomal dominant mode. Five of these individuals had clinical manifestations of muscle disease phenotypically consistent with Emery‐Dreifuss muscular dystrophy. Genetic analysis of this kindred had demonstrated a nonsense mutation in the LMNA gene located on chromosome 1q11–q23. This gene encodes lamins A and C, proteins of the nuclear lamina located on the inner face of the nuclear envelope. We retrospectively determined the cause of death of 15 deceased family members, 8 of whom had died suddenly, 2 as a first and single manifestation of the disease. The six other cases had histories of arrhythmias and left ventricular dysfunction before dying suddenly, and three of them died despite the prior implantation of a permanent pacemaker. The mean age of onset of cardiac symptoms among affected living family members was 33 years (range 15–47 years), and the first symptoms were due to marked atrioventricular conduction defects or sinus dysfunction, requiring the implantation of permanent pacemakers in seven cases. Myocardial dysfunction accompanied by ventricular arrhythmias developed rapidly in the course of the disease and resulted in severe dilated cardiomyopathy requiring cardiac transplantation in three cases. In conclusion, in patients presenting a life‐threatening familial or sporadic cardiac restricted phenotype similar to that described here, mutations in the lamins A and C gene should be looked for. In the genotypically affected individuals, cardiological and electrophysiological follow‐up should be performed to prevent sudden death that could occur rapidly in the evolution of such disease.
Overproduction of a conserved domain of fission yeast and mammalian translation initiation factor eIF4G causes aberrant cell morphology and results in disruption of the localization of F‐actin and the organization of microtubules

Background: The recruitment of mRNA for translation involves the assembly at the 5′cap of a complex of three initiation factors: the cap binding protein eIF4E, the ATP‐dependent RNA helicase eIF4A and the scaffold protein eIF4G. eIF4G mediates the binding of this mRNA–protein complex to the 43S ribosomal preinitiation complex. There is growing recognition that the components of the translational apparatus interact functionally with cytoskeletal components. Here we report specific effects of the over‐expression of human and fission yeast eIF4G domains on cell morphology in Schizosaccharomyces pombe.
Immunoblot analysis of sera in uncomplicated typhoid fever & with typhoid ileal perforation.

BACKGROUND & OBJECTIVE Ileal perforation is a serious complication of typhoid fever. The exact reasons for the development of perforation in only a few of those infected with Salmonella Typhi is unknown, and it is likely that immunological factors are involved. Therefore we undertook this study to compare the antibody profile in patients with uncomplicated typhoid fever with those having ileal perforation by immunoblotting. METHODS Two groups of patients were included in the study. Group II comprised patients with uncomplicated typhoid fever (n=47), and group I with typhoid ileal perforation (n=33). The flagellar (H), lipopolysaccharide (LPS) and outer membrane protein (OMP) antigens of Salmonella Typhi were extracted and used to test patient sera for antibodies by immunoblotting RESULTS Immunoblotting using S. Typhi antigens enabled the detection of S. Typhi antibodies in the two groups of patients. A significant difference was seen in the response of these two groups of patients with respect to antibodies to flagella, lipopolysaccharide and outer membrane proteins. Antibodies to flagella were more pronounced among patients with uncomplicated typhoid fever, while anti-OMP antibodies were significantly associated with typhoid ileal perforation. INTERPRETATION & CONCLUSION A comparison of antibodies in patients with uncomplicated typhoid fever and with ileal perforation revealed the differences in the antibody profiles of the two groups. Our study suggests that the difference in antibody response may in some way play a role in the pathogenesis of typhoid ileal perforation which can also potentially be exploited to develop suitable diagnostic tests.
Intraoperative frozen section analysis of sentinel lymph nodes in breast cancer patients

Accurate intraoperative pathologic examination of sentinel lymph nodes (SLNs) has been an important tool that can reduce the need for reoperations in patients with SLN‐positive breast cancer. The objective of the current study was to determine the accuracy of intraoperative frozen section (IFS) of SLNs during breast cancer surgery.
Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L

Auxin is the major regulator of plant growth and development. It regulates gene expression via a family of transcription factors (ARFs) that bind to auxin responsive elements (AuxREs) in the gene promoters. The canonical AuxREs found in regulatory regions of many auxin responsive genes contain the TGTCTC core motif, whereas ARF binding site is a degenerate TGTCNN with TGTCGG strongly preferred. Thereby two questions arise: which TGTCNN variants are functional AuxRE cores and whether different TGTCNN variants have distinct functional roles? In this study, we performed meta-analysis of microarray data to reveal TGTCNN variants essential for auxin response and to characterize their functional features. Our results indicate that four TGTCNN motifs (TGTCTC, TGTCCC, TGTCGG, and TGTCTG) are associated with auxin up-regulation and two (TGTCGG, TGTCAT) with auxin down-regulation, but to a lesser extent. The genes having some of these motifs in their regulatory regions showed time-specific auxin response. Functional annotation of auxin up- and down-regulated genes also revealed GO terms specific for the auxin-regulated genes with certain TGTCNN variants in their promoters. Our results provide an idea that various TGTCNN motifs may play distinct roles in the auxin regulation of gene expression.
Antiphospholipid Antibodies and the Antiphospholipid Syndrome in Systemic Lupus Erythematosus A Prospective Analysis of 500 Consecutive Patients

Five hundred consecutive patients with systemic lupus erythematosus (SLE) were entered into a prospective study of anticardiolipin antibodies (ACLA) in their 3 major immunoglobulin isotypes and followed thereafter with repeated testing for a mean period of nearly 8 months. Manifestations of SLE that were strongly associated with ACLA included venous thrombosis (particularly when recurrent), thrombocytopenia, hemolytic anemia, recurrent fetal loss, and leg ulcers. Other manifestations found to be associated with ACLA were arterial occlusions, transverse myelitis, and pulmonary hypertension. Conversely, we found no relationship between ACLA and migraine, convulsions, transient ischemic attacks, psychoses, or avascular necrosis of bone. No relationship was found between the presence of ACLA and that of anti-DNA antibodies studied in the same serum sample. Association with ACLA grew stronger and titers became higher in patients with several of the associated manifestations. Statistical analyses revealed the existence of a syndrome, the antiphospholipid syndrome, comprising 2 or more manifestations in conjunction with ACLA titers 5 standard deviations above the mean of normal control subjects, particularly if ACLA had been positive on at least 2 occasions. We propose that such criteria could be applied to the definition of the antiphospholipid syndrome. The presence and the titers of these antibodies related to disease activity and titer decreased by treatment, particularly when they were of the IgM isotype. Patients in whom a thrombotic episode occurred during the course of the study were observed to have a coincident decrease in ACLA titers, a finding that might indicate consumption of the antibody during the event. Treatment and the resulting inactivation of disease appear to have independent effects on ACLA titers. Physicians should therefore be cautious in prescribing high doses of corticosteroids or immunosuppressants to patients with SLE solely because they have high titers of ACLA.
Risk taking during decision-making in normal volunteers changes with age

Risk taking in a large cohort of adults (N = 177; ages 17–73) decreased with age, demonstrated by performance on a computer based gambling task, which has previously been shown to be sensitive to certain pharmacological manipulations including tryptophan depletion, lesions of the orbitofrontal cortex and neuropsychiatric disorders such as mania. Aging was also associated with longer deliberation times, poorer decision making, reduced risk taking, but no significant change in delay aversion. Subjects with a higher (NART-estimated) IQ were faster to make decisions and showed a greater modulation of risk-taking. Both sexes showed similar patterns of decision making, although male participants exhibited a greater modulation of risk-taking in response to the probability of winning. The Decision-Gamble task provides a variety of behavioral measures, corresponding to different aspects of impulsivity. Factor analysis of these measures suggested that two independent traits underlies performance on the task in normal individuals: one associated with risk tolerance, and a second associated with delay aversion. Age was related to decreases in the risk tolerance factor, but unrelated to the delay aversion; neither factor was significantly related to verbal IQ. This study thus provides support for the concept that impulsivity can be fractionated into 2 or more components. (JINS, 2004, 10, 590–598.)
The Use of Electrodermal Responses in a Case of Amnesia (A Case Report)

This article presents an attempt to use an electrodermal apparatus in order to establish the identity of an amnesic patient. By employing items of high personal relevance it proved possible to detect some useful information from the patient, although she claimed to be unaware of the information sought. There was a marked increase in electrodermal responsivity to items of personal relevance as the patient admitted more awareness of her past history, suggesting that detect-ability may improve with heightened conscious awareness.
Plasmodium vivax parasites alter the balance of myeloid and plasmacytoid dendritic cells and the induction of regulatory T cells

Immunity induced by Plasmodium vivax infections leads to memory T‐cell recruitment and activation during subsequent infections. Here, we investigated the role of regulatory T cells (Treg) in coordination with the host immune response during P. vivax infection. Our results showed a significant increase in the percentage of FOXP3+ Treg, IL‐10‐secreting Type I Treg (Tr1) and IL‐10 levels in patients with acute P. vivax infection as compared with those found in either naïve or immune controls. The concurrent increase in the Treg population could also be reproduced in vitro using peripheral blood mononuclear cells from naïve controls stimulated with crude antigens extracted from P. vivax‐infected red blood cells. Acute P. vivax infections were associated with a significant decrease in the numbers of DC, indicating a general immunosuppression during P. vivax infections. However, unlike P. falciparum infections, we found that the ratio of myeloid DC (MDC) to plasmacytoid DC (PDC) was significantly lower in acute P. vivax patients than that of naïve and immune controls. Moreover, the reduction in PDC may be partly responsible for the poor antibody responses during P. vivax infections. Taken together, these results suggest that P. vivax parasites interact with DC, which alters the MDC/PDC ratio that potentially leads to Treg activation and IL‐10 release.
To Go or Not To Go? A Near Unsupervised Learning Approach For Robot Navigation

It is important for robots to be able to decide whether they can go through a space or not, as they navigate through a dynamic environment. This capability can help them avoid injury or serious damage, e.g., as a result of running into people and obstacles, getting stuck, or falling off an edge. To this end, we propose an unsupervised and a near-unsupervised method based on Generative Adversarial Networks (GAN) to classify scenarios as traversable or not based on visual data. Our method is inspired by the recent success of data-driven approaches on computer vision problems and anomaly detection, and reduces the need for vast amounts of negative examples at training time. Collecting negative data indicating that a robot should not go through a space is typically hard and dangerous because of collisions, whereas collecting positive data can be automated and done safely based on the robot's own traveling experience. We verify the generality and effectiveness of the proposed approach on a test dataset collected in a previously unseen environment with a mobile robot. Furthermore, we show that our method can be used to build costmaps (we call as "GoNoGo" costmaps) for robot path planning using visual data only.
Quantification of venous vessel size in human brain in response to hypercapnia and hyperoxia using magnetic resonance imaging

Hypercapnia and hyperoxia give rise to vasodilation and vasoconstriction, respectively. This study investigates the influence of hypercapnia and hyperoxia on venous vessel size in the human brain. Venous vessel radii were measured in response to hypercapnia and hyperoxia. The venous vessel radii were determined by calculation of the changes in R2* and R2 that are induced by breathing 6% CO2 or pure oxygen. The experimental paradigm consisted of two 3‐min intervals of inhaling 6% CO2 or 100% O2 interleaved with three 2‐min intervals of breathing air. Hypercapnic and hyperoxic experiments were performed on eight subjects on a 3T scanner. Parametric maps of mean venous vessel radius were calculated from the changes in R2* and R2, which were measured by simultaneous acquisition of gradient‐echo and spin‐echo signals. The mean venous vessel radii in hypercapnia were 7.3 ± 0.3 μm in gray matter and 6.6 ± 0.5 μm in white matter. The corresponding vessel radii in hyperoxia were 5.6 ± 0.2 μm in gray matter and 5.4 ± 0.2 μm in white matter. These results show that the venous vessel radius was larger in hypercapnia than that in hyperoxia in both gray matter and white matter (P < 0.005), which agrees with the hypothesis that hypercapnia causes vasodilation and hyperoxia induces vasoconstriction. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Purification, Characterization, and Potential Bacterial Wax Production Role of an NADPH-Dependent Fatty Aldehyde Reductase from Marinobacter aquaeolei VT8

ABSTRACT Wax esters, ester-linked fatty acids and long-chain alcohols, are important energy storage compounds in select bacteria. The synthesis of wax esters from fatty acids is proposed to require the action of a four-enzyme pathway. An essential step in the pathway is the reduction of a fatty aldehyde to the corresponding fatty alcohol, although the enzyme responsible for catalyzing this reaction has yet to be identified in bacteria. We report here the purification and characterization of an enzyme from the wax ester-accumulating bacterium Marinobacter aquaeolei VT8, which is a proposed fatty aldehyde reductase in this pathway. The enzyme, a 57-kDa monomer, was expressed in Escherichia coli as a fusion protein with the maltose binding protein on the N terminus and was purified to near homogeneity by using amylose affinity chromatography. The purified enzyme was found to reduce a number of long-chain aldehydes to the corresponding alcohols coupled to the oxidation of NADPH. The highest specific activity was observed for the reduction of decanal (85 nmol decanal reduced/min/mg). Short-chain and aromatic aldehydes were not substrates. The enzyme showed no detectable catalysis of the reverse reaction, the oxidation of decanol by NADP+. The mechanism of the enzyme was probed with several site-specific chemical probes. The possible uses of this enzyme in the production of wax esters are discussed.
Screening the 3′ region of the polycystic kidney disease 1 (PKD1) gene in 41 Bulgarian and Australian kindreds reveals a prevalence of protein truncating mutations

Screening for disease‐causing mutations in the unique region of the polycystic kidney disease 1 (PKD1) gene was performed in 41 unrelated individuals with autosomal dominant polycystic kidney disease. Exons 34‐41 and 43‐46 were assayed using PCR amplification and SSCP analysis followed by direct sequencing of amplicons presenting variant SSCP patterns. We have identified seven disease‐causing mutations of which five are novel [c.10634‐10656del; c.11587delG; IVS37–10C>A; c.11669‐11674del; c.13069‐13070ins39] and two have been reported previously [Q4010X; Q4041X]. Defects in this part of the gene thus account for 17% of our group of patients. Five of the seven sequence alterations detected are protein‐truncating which is in agreement with mutation screening data for this part of the gene by other groups. The two other mutations are in‐frame deletions or insertions which could destroy important functional properties of polycystin 1. These findings suggest that the first step toward cyst formation in PKD1 patients is the loss of one functional copy of polycystin 1, which indirectly supports the “two‐hit” model of cystogenesis where a second somatic mutation inactivating the normal allele is necessary to occur for development of the disease condition. Hum Mutat 16:166–174, 2000. © 2000 Wiley‐Liss, Inc.
Development of an Automatic Electrical Stimulator for Mushroom Sawdust Bottle

In is well known among mushroom farmers that many mushrooms extraordinarily grow within several tens of meters around the spot where lightning strikes. It is supposed that the electrical stimulus of thunderbolts into myceliated logs accelerates the generation or development of mushrooms. Unfortunately, we cannot control natural thunderbolts but we can create artificial thunderbolts such as the pulsed high voltages of pulsed power technology. We started this study in 2002 and reported at PPC 2003 about the effect of an increase in production of shiitake mushrooms. The results showed that the yield from logs to which pulsed high voltage was applied was twice as great as those that received no electrical stimulus. [1]. Although mushrooms have been cultured in the forest using oak logs since old times, automated indoor production is today's standard. The room temperature and humidity in mushroom factories can be suitably controlled. Bottles nested in trays are filled with sawdust and other materials, inoculated with mushroom mycelium, incubated, and finally grown and harvested. In this paper some experiments to increase production of mushrooms from sawdust bottles are described. After the experiments, an electrical stimulator was finally designed and installed at a mushroom factory in February 2005. Pulsed high voltages up to 140 kV were applied to sawdust bottles as an electrical stimulus. Application of pulsed high voltages increased the yield of mushrooms by 13 to 15 percent compared with mushrooms to which it was not applied.