Miracle-dz/UniFAR-FTUs huggingface dataset:
Ancient and recent horizontal transfer events: The origins of Mitochondria

We have recently determined the genome sequence of Rickettsia prowazekii (Anderson et al., 1998). One of our primary aims in this work was to explore the phylogenetic relationship between this bacterium and the mitochondria. Our analysis of this putative relationship has led to confrontations with the potential effects of horizontal gene transfer on three levels: One of these is the presence of what may be “alien” (recent horizontally transferred) genes in the Rickettsia genome. Another, is the massive transfer of genes from an intracellular ancestor ofthe mitochondria to the nuclear genome of an ancient eukaryote. The third is the conjecture that high frequency horizontal transfer during the evolution of the progenote ancestor (Woese, 1998) generated the highly conserved ancient gene clusters that are extant in prokaryote genomes. Accordingly, we describe here aspects of the Rickettsia genome and its relationship to the mitochondria with a focus on the impact of horizontal transfer on this evolutionary relationship. The genome sequence of Rickettsia prowazekii, the agent of typhus in humans, features a number of oddities (Anderson et al., 1998). Among these is the presence of coding sequences with close affinities to orthologs found in genomes quite distant phylogenetically from those of bacteria. There are also scrambled versions of normally conserved ancient motifs and a generous investment in non-coding sequence. All of this is packaged within a modest 1.1 million base pairs. In our view these oddities reflect in some ways the evolutionary trajectory of this particular alpha-proteobacterium, and in others, the inevitable fate of endocellular parasites. In order to demystifi some of the quirks of this little genome we need to bring together several new developments bearing on the origins and metastability of the conserved gene orders characteristic of archaeal and bacterial genomes. The views of C. R. Woese (1998) on the early evolution of the “common ancestor” provide a platform for a discussion of the role of intensive horizontal gene transfer in generating highly conserved gene orders. We contrast this process with the dissolution of ancient motifs as well as the neutralization of coding sequences in genomes such as that of R. prowazekii. Here, we emphasize the distinction between the mechanisms that generate coherent genomic architectures; those that maintain them and those that transfer them from genome to genome. To account for the dissolution of architectural coherence along with other features of the highly derived Rickettsia genome we take up the special constraints on the population structure of endocellular parasites. The bottlenecked population dynamic that has dominated the genome evolution of endocellular parasites has shaped mitochondria as well (Kurland, 1992; Anderson and Kurland, 1998). Indeed, the genomes of mitochondria may be viewed as more extreme versions of such highly derived and diminished ones such as those of
The risk of cutaneous adverse reactions among patients with the HLA-A* 31:01 allele who are given carbamazepine, oxcarbazepine or eslicarbazepine: a perspective review

Carbamazepine is a drug that is widely used for the treatment of epilepsy, trigeminal neuralgia and bipolar disorder. This drug is also known to cause cutaneous adverse drug reactions (cADRs) in up to 10% of patients. The recent progress in pharmacogenetics has revealed that human leukocyte antigen (HLA) genotypes are associated with a susceptibility to the cADRs caused by particular drugs. For carbamazepine-induced Stevens–Johnson syndrome and toxic epidermal necrolysis, very strong associations with HLA-B*15:02 have been found mainly in patients of Southeastern Asian origin. In some countries, prescreening HLA-B*15:02 allele has already been put to practical use as a biomarker to avoid the life-threatening adverse drug reactions. In this review, another risk factor for carbamazepine-induced cADRs is discussed, namely HLA-A*31:01. We compare the strength of the association between HLA-A*31:01 and carbamazepine-induced cADRs based on reports for various ethnic populations; discuss the difference between the HLA-A*31:01 and HLA-B*15:02 biomarkers and the usefulness of prescreening HLA-A*31:01 to detect patients at high risk for carbamazepine-induced cADRs; and refer to points that remain to be resolved.
Evolution des paramètres acoustiques des bétons de chanvre sous l'effet du compactage

Hemp concrete is a porous concrete that can be used as an interesting alternative to traditional materials used in buildings. To control and optimise its acoustical behavior, it is important to predict the performance of this material as a function of the main parameters of its fabrication process. The study presented here aimed at determining the relationships between the acoustical parameters used in the models and the intrinsic parameters of the constituents and of the fabrication process. Mots clefs : Béton de chanvre ; Matériaux multi-échelles ; Paramètres acoustiques
Protective action of hepatocyte growth factor on transforming growth factor beta-1-induced alpha-smooth muscle actin and extracellular matrix in cultured human peritoneal fibroblasts.

BACKGROUND Peritoneal adhesion is the leading cause of severe mechanical bowel obstruction, female infertility, pelvic pain, and difficult surgical procedures. TGF-beta1 plays an important role in matrix production associated with postoperative peritoneal adhesion development. Recent investigators have shown that HGF works on several organs and has been given widespread attention because it has proved to have strong antifibrotic activity. The aim of this study was to determine the impact of HGF on markers of adhesion formation induced by TGF-beta1 in human peritoneal fibroblasts. MATERIAL/METHODS Fibroblasts were collected from normal peritoneum and were cultured with 5 ng/ml of TGF-beta1 along with increasing doses of HGF (10-40 ng/ml). Expression of alpha-SMA was assessed by Western blot. The productions of collagen I and fibronectin in supernatants culture were examined by enzyme-linked immunosorbent assay (ELISA). RESULTS TGF-beta1 significantly stimulated alpha-SMA, collagen I and fibronectin production in peritoneal fibroblasts. Remarkably, the addition of HGF reduced production of all components induced by TGF-beta1 in a dose-dependent manner. CONCLUSIONS This study suggests that HGF may be a novel, highly efficacious agent in the minimization of intra-abdominal adhesion. Although further studies are needed to assess the mechanisms of HGF in neutralizing the effect of TGF-beta1, these findings also provide a cellular and molecular basis for the action of HGF as an anti-adhesion agent.
Efficiency of Trained Cyclists Using Circular and Noncircular Chainrings

The purpose of this study was to determine oxygen consumption (VO2), heart rate (HR) response, and rating of perceived exertion (RPE) of trained cyclists using noncircular and circular chainrings over a range of gears and pedal cadences. The subjects included 7 male cyclists (6 USCF licensed riders, 1 national qualifying triathlete). Each subject rode his own bicycle mounted on a wind-trainer at gears of 5.92 and 7.33 meters with noncircular and circular chainrings at pedal cadences of 50, 70, and 90 rpm. VO2, HR, RPE, and respiratory exchange ratio (RER) measurements were made during each of the 12 rides. Mean percent VO2max for each condition ranged from 28.7 +/- 2.1% with the 5.92 meter gear at 50 rpm to 83.4 +/- 4.3% using the 7.33 meter gear at 90 rpm. The results indicate no significant difference in any of the parameters measured between the two chainrings for any of the experimental conditions. The data indicate that the noncircular chainrings used in this study were not more efficient than the standard circular chainring for trained cyclists.
Early muscle and brain ultrastructural changes in polymerase gamma 1‐related encephalomyopathy

Mutations affecting the mitochondrial DNA‐polymerase gamma 1 (POLG1) gene have been shown to cause Alpers‐Huttenlocher disease. Ultrastructural data on brain and muscle tissue are rare. We report on ultrastructural changes in brain and muscle tissue of two sisters who were compound heterozygous for the c.2243G>C and c.1879C>T POLG1 mutations. Patient 1 (16 years) presented with epilepsia partialis continua that did not respond to antiepileptic treatment. Neuroimaging showed right occipital and bithalamic changes. Light microscopy from a brain biopsy performed after 3 weeks suggested chronic encephalitis showing astro‐ and microgliosis as well as perivascular CD8‐positive T‐cells. However, immunosuppressive therapy failed to improve her condition. When her 17‐year‐old sister (patient 2) also developed epilepsy, an intensified search for metabolic diseases led to the diagnosis. On electron microscopy mitochondrial abnormalities mainly affecting neurons were detected in the brain biopsy of patient 1, including an increase in number and size, structural changes and globoid inclusions. In patient 2, light and electron microscopy on a muscle biopsy confirmed a mitochondrial myopathy, also revealing an increase in mitochondrial size and number, as well as globoid inclusions. Neurons may be the primary target of mitochondrial dysfunction in brains of patients with Alpers disease related to POLG1 mutations. During early disease stages, brain histopathology may be misleading, showing reactive inflammatory changes.
Psychosocial Factors Related to Cannabis Use Disorders

The objective of this study was to explore the association between psychosocial risk and protective factors and cannabis use disorders (CUDs) in a cohort of African American and Puerto Rican young adults. A representative sample (N = 838) from the East Harlem area of New York City was assessed at 4 points in time (at mean ages 14.1, 19.2, 24.5, and 29.2). The psychosocial measures came from 6 domains: personality attributes, family, peer, work, neighborhood, and substance use. The psychosocial measures were assessed at each of the first 3 waves of the study, and CUDs were assessed at the fourth and final wave of the study. Multivariate logistic regression and a cumulative risk analysis were conducted. Increased psychological symptoms (odds ratio [OR] = 1.21; 95% confidence interval [CI], 1.05–1.39; P < .01), problems resulting from cannabis use (OR = 2.69; 95% CI, 1.33–5.46; P < .01), frequent arguments with one's partner (OR = 1.84; 95% CI, 1.09–3.10; P < .05), high levels of deviance (OR = 1.81; 95% CI, 1.21–2.71; P < .01), and frequent acts of violence directed toward the participant (OR = 1.19; 95% CI, 1.01–1.42; P < .05) were all associated with an increased risk for CUDs. An increase in the number of risks was associated with an increase in the probability of having CUDs at the fourth wave (again, at a mean age of 29.2). A decrease in the number of risk factors may lead to a decrease in CUDs.
A miniaturized monolithic dual band filter using ceramic lamination technique for dual mode portable telephones

A miniaturized monolithic dual band filter is developed for dual mode portable telephones. By using a ceramic lamination technique, a 1 mm-thick 900 MHz filter and a 1.9 GHz filter are fabricated and stacked to be co-fired. The performance degradation due to the thickness and the dual band matching network are discussed. An experimental filter is constructed and shows very good performance.
Trauma patients without a trauma diagnosis: the data gap at a level one trauma center.

BACKGROUND Trauma registries may contain records without a codable trauma diagnosis, creating a "data gap" that multiplies the number of invalid registry data fields. We designed an investigation intended to determine the incidence of registry records with noncodable trauma diagnoses, characterize those records, and determine the reasons for inadequate diagnosis data. METHODS We used a retrospective cohort design. A query of trauma registry records spanning a 5-year period yielded 129 records with no injury severity score. Each patient's medical record was reviewed, sources of diagnostic information were noted, and diagnoses were categorized. RESULTS In 57% of cases, we found documentation that the patient had sustained an injury, but the injury was inadequately documented in the discharge summary. In 19% of cases, although the registry record was valid, the diagnosis was not codable as trauma. In 17% of cases, clinical documentation was adequate, but the diagnosis was inadequately recorded in the trauma registry. In 13% of cases, no traumatic injury was sustained, although the registry record was valid. In 2% of cases, the trauma registry record itself was invalid. In 1% of cases, a coding error occurred. Particularly prominent among records with inadequate discharge documentation were cases of head and spine injury for which there was no radiographic evidence. CONCLUSIONS The incidence of records with noncodable diagnoses might best be reduced through improved physician documentation, revision of trauma registry inclusion criteria, increased attention by trauma registrars to key sources of documentation, and direct communication with the attending physician when necessary.
Why Developers Are Slacking Off: Understanding How Software Teams Use Slack

Slack is a modern communication platform for teams that is seeing wide and rapid adoption by software develop-ment teams. Slack not only facilitates team messaging and archiving, but it also supports a wide plethora of inte-grations to external services and bots. We have found that Slack and its integrations (i.e., bots) are playing an increas-ingly significant role in software development, replacing email in some cases and disrupting software development processes. To understand how Slack impacts development team dynamics, we designed an exploratory study to inves-tigate how developers use Slack and how they benefit from it. We find that developers use Slack for personal, team-wide and community-wide purposes. Our research also reveals that developers use and create diverse integrations (called bots) to support their work. This study serves as the first step towards understanding the role of Slack in sup-porting software engineering.
One‐to‐all broadcasting scheme for arbitrary static interconnection networks with bursty background traffic

A novel one‐to‐all broadcasting scheme is proposed for arbitrary static interconnection networks with bursty background traffic having head‐of‐line priorities, complete buffer sharing and repetitive service blocking with random destination. The scheme facilitates inter‐process communication amongst parallel computers and grid computing networks as well as asynchronous transfer mode space division architectures and it is applicable to a single‐port mode of message passing communication. The scheme utilizes a queue‐by‐queue decomposition algorithm for arbitrary open queueing network models, based on the principle of maximum entropy, in conjunction with an information theoretic decomposition criterion and graph theoretic concepts. Evidence based on empirical studies indicates the suitability of the scheme for achieving an optimal one‐to‐all broadcasting cost. Copyright © 2004 John Wiley & Sons, Ltd.
In reply to: Lawless et al. Stalk versus base invasion in pT1 papillary cancers of the bladder: improved substaging system predicting the risk of progression

We read with interest the paper by M. Lawless et al. very recently published in Histopathology (Stalk versus base invasion in pT1 papillary cancers of the bladder: improved substaging system predicting the risk of progression) (1). The Authors divided tumors into base-focal and base-extensive cases, relying on the criterion of whether or not there was a single focus <1 mm in size (i.e. 20x PF), thus confirming the threshold adopted in our study on pT1 bladder urothelial carcinoma (2), kindly quoted by M. Lawless et al. This size enabled patient stratification in terms of risk of progression in both studies (1,2), and in others too (3), underscoring the value of T1 substaging recently emerging from a broad meta-analysis (4). This article is protected by copyright. All rights reserved.
Human APOBEC3F Is Another Host Factor That Blocks Human Immunodeficiency Virus Type 1 Replication

ABSTRACT Recently, APOBEC3G has been identified as a host factor that blocks retroviral replication. It introduces G to A hypermutations in newly synthesized minus strand viral cDNA at the step of reverse transcription in target cells. Here, we identified the human APOBEC3F protein as another host factor that blocks human immunodeficiency virus type 1 (HIV-1) replication. Similar to APOBEC3G, APOBEC3F also induced G to A hypermutations in HIV genomic DNA, and the viral Vif protein counteracted its activity. Thus, APOBEC family members might have evolved as a general defense mechanism of the body against retroviruses, retrotransposons, and other mobile genetic elements.
Inference about Multiple Pathways in Motor Control Limb in Locust

In locust local circuits that control limb movements, the neural signals are processed by both spiking and nonspiking interneurons that operate in parallel to process sensory information. These interneurons receive sensory inputs from leg mechanoreceptors and together project to leg motor neuron pools. The main feature of the nonspiking interneurons is their ability to communicate with other neurons without the intervention of nerve impulses, or spikes, so that they exert graded control over their postsynaptic motor neurons, while spiking local interneurons communicate by means of action potentials and are involved in the integration of sensory signals. Our work presents an investigation from different classes of neurons driven by random Gaussian excitatory movements to a proprioceptor at the knee joint. The underlying aim of this work was to use information theory in understanding connectivity in the neural network.
Evolution of residual stress and crack morphologies during 3D FIB tomographic analysis of alumina

Three‐dimensional focused ion beam (FIB) tomography is increasingly being used for 3D characterization of microstructures in the 50 nm–20 μm range. FIB tomography is a destructive, invasive process, and microstructural changes may potentially occur during the analysis process. Here residual stress and crack morphologies in single‐crystal sapphire samples have been concurrently analyzed using Cr3+ fluorescence spectroscopy and FIB tomography. Specifically, maps of surface residual stress have been obtained from optically polished single‐crystal alumina [surface orientation (1 ī 0 2)], from FIB milled surface trenches, from Vickers micro‐indentation sites (loads 50 g–300 g), and from Vickers micro‐indentation sites during FIB serial sectioning. The residual stress maps clearly show that FIB sputtering generates residual stress changes. For the case of the Vickers micro‐indentations, FIB sputtering causes significant changes in residual stress during the FIB tomographic serial sectioning. 3D reconstruction of the crack distribution around micro‐indentation sites shows that the cracks observed are influenced by the location of the FIB milled surface trenches due to localized stress changes.
INTERACTIONS OF BEHAVIORAL EFFECTS OF DRUGS

Interest in the joint effects of two drugs administered simultaneously is as old as scientific pharmacology. Frazer’ systematically explored the joint effects of physostigmine and atropine, and Bernard’ studied the effects of curare and (without knowing it) acetylcholine. The general pharmacological principles for assessment of joint effects are also of some antiquity and are widely accepted among pharmacologists, although there has been bickering, of course, about nomenclature. As good a scheme as any was provided by Gaddum3 over 35 years ago (FIGURE 1 ) . It is presented here as a reminder of a principle not infrequently overlooked by nonpharmacologists: Both dose and effect must be taken into account in determining the nature of the joint action of two drugswhether they are antagonistic or synergistic. If drug A in dose a causes effect of intensity x and drug B in dose b causes the same effect of intensity y , the joint effect of drugs A and B taken simultaneously in doses a and b would not be expected, in general, to be of intensity x + y . The reason that effects are not simply algebraically additive, even for drug pairs whose effects arc strictly additive in Gaddum’s sense, has been emphasized repeatedly: Dose-effect curves are generally not straight lines through the origin. When either a threshold
Patients' evaluation of outpatient medical care.

150 patients attending an outpatient clinic at the University of Oklahoma Hospital over a 5-week period were asked whether the clinic care they were receiving was better than, as good as, or worse than the care they had received from local physicians. The patients were drawn from the general medicine, cardiology, and oncology-hematology units and tended to be elderly and chronically ill. Most of the patients viewed favorably the care they received in the medical outpatient clinics. 65% reported they had experienced pain or discomfort in the week prior to their visit, but there was no association between these factors and degree of satisfaction with clinic care. Patients averaged about 30 minutes with the physician, and 80% felt the doctor adequately explained their medical condition to them. Patients who rated the clinic care as being worse than the care of private practitioners felt that their condition was not adequately explained. When asked to define a "good doctor," patient responses were "interest in the patient," "skilled and thorough," and "explains things to you. " Characteristics identified as being most important in a "good clinic" were; good doctors, well-trained staff, and information from doctors. Of all the factors examined, the one associated most directly with patient satisfaction was personal interest on the part of the physician in the patients.
A dielectric rod antenna as a high efficiency feed for reflector antennas

Radiation characteristics of a short dielectric rod antenna excited by a circular waveguide is investigated experimentally. It is found that, by a proper selection of the waveguide radius and the exposed length of dielectric rod, the E and H plane radiation patterns, the side and back radiations and the bandwidth of the antenna can be controlled. Some experimental data are presented and the usefulness of this antenna as a feed for paraboloidal reflectors is also discussed.
Developing a Tool for Remote Digital Assessment of Parkinson's Disease

The natural fluctuation of motor symptoms of Parkinson's disease (PD) makes judgement of any change challenging and the use of clinical scales such as the International Parkinson and Movement Disorder Society (MDS)‐UPDRS imperative. Recently developed commodity mobile communication devices, such as smartphones, could possibly be used to assess motor symptoms in PD patients in a convenient way with low cost. We provide the first report on the development and testing of stand‐alone software for mobile devices that could be used to assess both tremor and bradykinesia of PD patients.
The Action of Pasteurella pestis Bacteriophage on Strains of Pasteurella, Salmonella, and Shigella

Bacteriophages active against Pasteurella pestis have been described by a number of workers, including Flu (1927), Sugino (1932), Advier (1933), and Girard (1942). The subject has been reviewed by Harvey (1933) and Wu et al. (1936). This report describes certain relationships of P. pestis to Pasteurella pseudotuberculosis and to Salmonella and Shigella strains, as shown by bacteriophage action and confirmed to a limited extent by agglutination tests.