Miracle-dz/UniFAR-FTUs huggingface dataset:
Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources

Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. Methodology/Principal Findings The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid). Conclusion/Significance These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
Long‐term administration of ddt or phenobarbital‐na in wistar rats

In lifespan studies, outbred male and female Wistar rats were given either technical DDT mixed into the diet at a dose of 500 parts per million (ppm) or phenobarbital‐sodium dissolved in drinking water at a dose of 500 ppm. Liver‐cell tumors developed in treated animals but not in controls. The incidence of liver tumors was 45% in the DDT‐treated group and 44% in the phenobarbital‐sodium‐group. When evaluated by sex, DDT‐treated females and males had incidences of 56% and 35%, respectively, while in the phenobarbital‐sodium group, the respective incidences were 32% and 59% in females and males. These data show a varying susceptibility between the sexes, with regard to induction of liver‐cell tumors by the two compounds. In both treated groups, the number of nodular tumors per rat and the average size increased with age and were greater in females. None of these tumors had metastasized. Histologically, the liver tumors were nodular growths, which compressed surrounding parenchyma but did not infiltrate it. The total incidence of extrahepatic tumors was higher in controls than in treated animals. In this connection, we must mention the apparent, but not significant, reduction of adrenal tumors in treated rats compared to the controls.
Allocating tasks to workers with matching constraints: truthful mechanisms for crowdsourcing markets

Designing optimal pricing policies and mechanisms for allocating tasks to workers is central to the online crowdsourcing markets. In this paper, we consider the following realistic setting of online crowdsourcing markets -- there is a requester with a limited budget and a heterogeneous set of tasks each requiring certain skills; there is a pool of workers and each worker has certain expertise and interests which define the set of tasks she can and is willing to do. Under the matching constraints given by this bipartite graph between workers and tasks, we design our incentive-compatible mechanism truthuniform which allocates the tasks to the workers, while ensuring budget feasibility and achieves near-optimal utility for the requester. Apart from strong theoretical guarantees, we carry out experiments on a realistic case study of Wikipedia translation project on Mechanical Turk. We note that this is the first paper to address this setting from a mechanism design perspective.
ISOLATION AND RAPID IDENTIFICATION OF CANDIDASPECIES FROM THE ORAL CAVITY

CHROMagar Candida is a new differential culture medium that allows the isolation and presumptive identification of species of yeast of clinical importance. During the past two decades, there has been a significant increase in the prevalence of fungal infections caused by Candida species. The aim of the study was to isolate and identify Candida species from the oral cavity with CHROMagar Candida. This study was carried out in 30 patients with infections aged 21 to 90 years. Swabs samples were taken from oral cavity and were cultured directly on Sabouraud dextrose agar medium. In this study shows that CHROMagar Candida can easily identify four species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida glabrata, Candida tropicalis and Candida krusei. Results showed the prevalence of C.albicans (n = 21, 70%), C. glabrata (n = 5, 16.6%), C. krusei (n = 2, 6.7%), and C. tropicalis (n =2, 6.7%). In this investigation, CHROMagar produced light green colonies and were considered as Candida albicans, Pink with a darker mauve center colonies were identified as Candida glabrata, pink with pale borders colonies were identified as Candida krusei, and dark blue, purple diffusion colonies were identified as Candida tropicalis. CHROMagar is extremely useful in making a rapid presumptive identification of common yeast species. This capability plus the ability to detect mixed cultures of Candida species promises to improve and streamline the work flow in the mycology and clinical microbiology laboratory.
Management of pleural infection in adults: British Thoracic Society pleural disease guideline 2010

Pleural infection is a frequent clinical problem with an approximate annual incidence of up to 80 000 cases in the UK and USA combined. The associated mortality and morbidity is high; in the UK 20% of patients with empyema die and approximately 20% require surgery to recover within 12 months of their infection.1 2 Prompt evaluation and therapeutic intervention appears to reduce morbidity and mortality as well as healthcare costs.3 This article presents the results of a peer-reviewed systematic literature review combined with expert opinion of the preferred management of pleural infection in adults for clinicians in the UK. The clinical guidelines generated from this process are presented in figure 1. The guidelines are aimed predominantly at physicians involved in adult general and respiratory medicine and specifically do not cover in detail the complex areas of tuberculous empyema, paediatric empyema or the surgical management of post-pneumonectomy space infection. Figure 1 Flow diagram describing the management of pleural infection. This section provides background information for reference, interest and to set the management guidelines in context. ### Historical perspective The Egyptian physician Imhotep initially described pleural infection around 3000 BC, although Hippocrates has been more famously credited with its recognition in 500 BC. Until the 19th century open thoracic drainage was the recommended treatment for this disorder but carried an associated mortality of up to 70%. 4 5 This high mortality was probably due to respiratory failure produced by the large open pneumothorax left by drainage.5 This was particularly true of Streptococcus pyogenes infections which produce streptokinase and large alocular effusions free of adhesions.5 Closed tube drainage was first described in 1876 but was not widely adopted until the influenza epidemic of 1917–19. An Empyema Commission subsequently produced recommendations that remain the basis for treatment today. They advocated adequate pus drainage with a closed …
A biomaterials approach to peripheral nerve regeneration: bridging the peripheral nerve gap and enhancing functional recovery

Microsurgical techniques for the treatment of large peripheral nerve injuries (such as the gold standard autograft) and its main clinically approved alternative—hollow nerve guidance conduits (NGCs)—have a number of limitations that need to be addressed. NGCs, in particular, are limited to treating a relatively short nerve gap (4 cm in length) and are often associated with poor functional recovery. Recent advances in biomaterials and tissue engineering approaches are seeking to overcome the limitations associated with these treatment methods. This review critically discusses the advances in biomaterial-based NGCs, their limitations and where future improvements may be required. Recent developments include the incorporation of topographical guidance features and/or intraluminal structures, which attempt to guide Schwann cell (SC) migration and axonal regrowth towards their distal targets. The use of such strategies requires consideration of the size and distribution of these topographical features, as well as a suitable surface for cell–material interactions. Likewise, cellular and molecular-based therapies are being considered for the creation of a more conductive nerve microenvironment. For example, hurdles associated with the short half-lives and low stability of molecular therapies are being surmounted through the use of controlled delivery systems. Similarly, cells (SCs, stem cells and genetically modified cells) are being delivered with biomaterial matrices in attempts to control their dispersion and to facilitate their incorporation within the host regeneration process. Despite recent advances in peripheral nerve repair, there are a number of key factors that need to be considered in order for these new technologies to reach the clinic.
Simple, Robust and Optimal Ranking from Pairwise Comparisons

We consider data in the form of pairwise comparisons of n items, with the goal of precisely identifying the top k items for some value of k < n, or alternatively, recovering a ranking of all the items. We analyze the Copeland counting algorithm that ranks the items in order of the number of pairwise comparisons won, and show it has three attractive features: (a) its computational efficiency leads to speed-ups of several orders of magnitude in computation time as compared to prior work; (b) it is robust in that theoretical guarantees impose no conditions on the underlying matrix of pairwise-comparison probabilities, in contrast to some prior work that applies only to the BTL parametric model; and (c) it is an optimal method up to constant factors, meaning that it achieves the information-theoretic limits for recovering the top k-subset. We extend our results to obtain sharp guarantees for approximate recovery under the Hamming distortion metric, and more generally, to any arbitrary error requirement that satisfies a simple and natural monotonicity condition.
Mutations in the familial Mediterranean fever gene of patients with IgA nephropathy and other forms of glomerulonephritis

Glomerulonephritis, particularly IgA nephropathy (IgAN), seems to be more common in familial Mediterranean fever (FMF), an inherited disease caused by mutations in the MEditerranean FeVer gene (MEFV). The present study is aimed to determine, in populations not suffering from FMF, whether carriage of MEFV mutations may modify or precipitate IgAN and other forms of primary glomerulonephritis (PGN). Forty patients with biopsy proven IgAN and 40 with PGN were surveyed for the presence of the three most common MEFV mutations (M694V, V726A and E148Q), using polymerase chain reaction amplification and restriction enzyme analysis. The rate of MEFV mutations in the patients was related to the expected carrier rate in the general population of the same ethnic extraction. The effect of mutation carriage on the disease course was determined in the IgAN patient group. The frequency of MEFV mutations in IgAN or PGN was comparable to that found in ethnically adjusted general population (p = 0.1 and 0.5, respectively). Carriage of mutated MEFV was not associated with the course and severity of the disease or findings in kidney biopsy and urine analysis. In a population, mostly of Jewish extraction, MEFV mutations do not seem to predispose to the development of IgAN and other forms of PGN or affect the phenotype.
P300 Source Localization Contrasts in Body-Focused Repetitive Behaviors and Tic Disorders

Tic disorders (TD) and body-focused repetitive behaviors (BFRB) have similar phenotypes that can be challenging to distinguish in clinical settings. Both disorders show high rates of comorbid psychiatric conditions, dysfunctional basal ganglia activity, atypical cortical functioning in the prefrontal and motor cortical regions, and cognitive deficits. Clinicians frequently confound the two disorders and it is important to find reliable objective methods to discriminate TD and BFRB. Neuropsychological tests and event-related potential (ERP) studies have yielded inconsistent results regarding a possible context updating deficit in TD and BFRB patients. However, most previous studies did not control for the presence of comorbid psychiatric condition and medication status, which might have confounded the findings reported to date. Hence, we aimed to investigate the psychophysiology of working memory using ERP in carefully screened TD and BFRB patients excluding those with psychiatric comorbidity and those taking psychoactive medication. The current study compared 12 TD patients, 12 BRFB patients, and 15 healthy control participants using a motor oddball task (button press). The P300 component was analyzed as an index of working memory functioning. Results showed that BFRB patients had decreased P300 oddball effect amplitudes over the right hemisphere compared to the TD and control groups. Clinical groups presented different scalp distributions compared to controls, which could represent a potential endophenotype candidate of BFRB and TD.
Complement and the damaging effects of cardiopulmonary bypass.

"One of the most serious difficulties encountered in total body perfusion is the profound effect upon the lungs that may occur in certain patients. It is indeed discouraging to perform open cardiac corrective surgery, to have the patient remain in excellent condition throughout the procedure and for a day or two thereafter, finally succumbing to pulmonary insufficiency while the heart itself remains strong to the very end. " F D DODRILI, Chicago, September 1957
LOCALIZATION OF MICROCYSTIN SYNTHETASE GENES IN COLONIES OF THE CYANOBACTERIUM MICROCYSTIS USING FLUORESCENCE IN SITU HYBRIDIZATION 1

To better understand the production of microcystins (MCs) in Microcystis colonies, fluorescence in situ hybridization (FISH) methods were developed to detect DNA involved in the synthesis of these cyanobacterial hepatotoxins. Using colonies of Microcystis aeruginosa (Kütz.) Kütz. isolated from environmental blooms of cyanobacteria and from a colony‐forming, MC‐producing laboratory strain of Microcystis, amplified PCR products were observed, coincident with positive controls. The total MC content of individual colonies of Microcystis, determined by ELISA, showed a positive correlation with colony cross‐sectional area. FISH analysis of Microcystis colonies gave high fluorescence in comparison to negative controls, indicating the presence of MC synthetase DNA (mcyA) in situ. FISH analysis for MC synthetase genes has the potential to be developed into an effective early warning tool for drinking and recreational water management.
Error probability bounds for balanced binary relay trees

We study the detection error probability associated with a balanced binary relay tree, where the leaves of the tree correspond to N identical and independent sensors. The root of the tree represents a fusion center that makes the overall detection decision. Each of the other nodes in the tree are relay nodes that combine two binary messages to form a single output binary message. Only the leaves of the tree are sensors. In this way, the information from the sensors is aggregated into the fusion center via the intermediate relay nodes. In this context, we describe the evolution of Type I and Type II error probabilities of the binary data as it propagates from the leaves towards the root. Tight upper and lower bounds for the total error probability at the fusion center as functions of N are derived. These characterize how fast the total error probability converges to 0 with respect to N.
Large-scale cooperative 3D visual-inertial mapping in a Manhattan world

In this paper, we address the problem of cooperative mapping (CM) using datasets collected by multiple users at different times, when the transformation between the users' starting poses is unknown. Specifically, we formulate CM as a constrained optimization problem, where each user's independently estimated trajectory and map are combined in a single map by imposing geometric constraints between commonly-observed point and line features. Furthermore, our formulation allows for modularity since new/old maps (or parts of them) can be easily added/removed with no impact on the remaining ones. Additionally, the proposed CM algorithm lends itself, for the most part, to parallel implementations, hence gaining in speed. Experimental results based on visual and inertial measurements collected from four users within two large buildings are used to assess the performance of the proposed CM algorithm.
An Assessment of Type-3 Clones as Detected by State-of-the-Art Tools

Code reuse through copying and pasting leads to so-called software clones. These clones can be roughly categorized into identical fragments (type-1 clones), fragments with parameter substitution (type-2 clones), and similar fragments that differ through modified,deleted, or added statements (type-3 clones). Although there has been extensive research on detecting clones, detection of type-3 clones is still an open research issue due to the inherent vaguenessin their definition. In this paper, we analyze type-3 clones detected by state-of-the-art tools and investigate type-3 clones in terms of their syntactic differences. Then, we derive their underlying semantic abstractions from their syntactic differences. Finally, we investigate whether there are any additional code characteristics that indicate that a tool-suggested clone candidate is a real type-3 clone from a human's perspective. Our findings can help developers of clone detectors to improve their tools.
DSM-IV alcohol dependence and marital dissolution: evidence from the National Epidemiologic Survey on Alcohol and Related Conditions.

OBJECTIVE The purpose of this study was to examine the cross-sectional and longitudinal associations among alcohol use disorder (AUD), stressful life events, and marital dissolution in a probability sample of adults. METHOD The National Epidemiologic Survey on Alcohol and Related Conditions is a prospective, longitudinal study of a probability sample of 43,083 adults 18 years of age and older living in the United States. The interval between Wave 1 (W1) and Wave 2 (W2) was approximately 3 years. Cross-sectional analyses included 32,359 adults ages 18 and older who were ever married at W1, and longitudinal analyses included 17,192 adults who were currently married at W1 and who completed relevant W2 measures. Participants completed inhome surveys conducted with computer-assisted personal interviewing. RESULTS Rates of lifetime marital dissolution were significantly higher among those with lifetime AUD (48.3%) than in those with no lifetime AUD (30.1%). The incidence of marital dissolution from W1 to W2 was 15.5% for those with a past-12-month AUD at W1, compared to 4.8% among those with no AUD. Proportional hazards regression analyses showed that past-12-month AUD, tobacco use disorder, other substance use disorder, stressful life events, older age at marriage, being married more than once, and being married to an alcoholic at W1 predicted greater hazards of marital dissolution at W2. These associations were not moderated by gender. CONCLUSIONS AUD and stressful life events predict subsequent marital dissolution independently of other substance use disorders, mood and anxiety disorders, and personality disorders. Results were discussed within the framework of the Vulnerability-Stress-Adaptation model of marriage.
Novel Non-isotopic Method for the Localization of Receptors in Tissue Sections

We describe a novel fluorescent method for the detection of receptors for chimeric proteins in tissue sections. The technique was developed using a recombinant human insulin-like growth factor (IGF-1) chimera, bearing six additional histidine residues at the carboxy-terminal end (IGF-1-His). We demonstrated that dehydration of the tissue sections was detrimental for binding and that its prevention dramatically increased sensitivity. The specificity of IGF-1-His interaction was shown by gradual abolition of the fluorescent signal in the presence of increasing concentrations of IGF-1. Combining immunofluorescence with in situ ligand binding, we showed that IGF-1-His binding corresponded to the IGF-1 receptor (IGFR-1) distribution in human fetal kidney. Moreover, incubation of the tissue sections with an anti-IGFR-1 blocking antibody abolished IGF-1-His binding, demonstrating that the interaction was mediated by the IGFR-1. The method was also used to localize the IGFR-1 in E18 rat embryo sagittal sections. The IGF-1-His binding pattern was observed in brain, cartilage, lung, skin, heart, diaphragm, and tongue, and paralleled the previously reported IGFR-1 distribution. We believe that this new non-isotopic in situ ligand binding method will facilitate rapid and accurate localization of receptors in tissue sections.
2 WORKING PAPER No . 11 / 2008 Strategic Use of Trust

While most of the previous literature interprets trust as an action, we adopt a view that trust is represented by a belief that the other party will return a fair share. The agent’s action is then a commitment device that signals this belief. In this paper we propose and test a conjecture that economic agents use trust strategically. That is, the agents have incentives to inflate the perceived level of trust (the signal) in order to induce a more favorable outcome for themselves. In the experiment we study the behavior of subjects in a modified investment game which is played sequentially and simultaneously. While the sequential treatment allows for strategic use of trust, in the simultaneous treatment the first mover’s action is not observed and hence does not signal her belief. In line with our prediction we find that first movers send significantly more in the sequential treatment than in simultaneous. Moreover, second movers reward trusting action, but only if it is maximal. We also find that signaling with trust enhances welfare.