Miracle-dz/UniFAR-FTUs huggingface dataset:
A field study with genetically engineered alfalfa inoculated with recombinant Sinorhizobium meliloti: effects on the soil ecosystem

Summary 1. A field study using transgenic plants with associated recombinant micro-organisms was conducted to assess the potential effects of genetically engineered organisms on soil ecosystems. Three genotypes of alfalfa plants (parental, transgenic α-amylase-producing and transgenic lignin peroxidase-producing) were planted in an agricultural field plot. Immediately prior to planting, the roots of the alfalfa plants were left uninoculated or were inoculated with a wild-type strain (PC), a recombinant strain with antibiotic resistances (RMB7201), or a recombinant strain with antibiotic resistances and enhanced nitrogen-fixation capability (RMBPC-2), of Sinorhizobium meliloti. 2. Analyses of the alfalfa plants and field plot soil were made over two growing seasons and included: metabolic fingerprints and DNA fingerprints of soil bacterial communities; soil microbial respiration; population counts of indigenous soil bacteria, fungi, nematodes, protozoa and micro-arthropods; identification of nematodes and micro-arthropods; plant shoot weight and chemistries; and soil chemistries and enzyme activities. 3. The lignin peroxidase transgenic plants had significantly lower shoot weight, and higher nitrogen and phosphorus content, than the parental or transgenic amylase plants. Distinct metabolic fingerprints, based on patterns of substrate utilization in Biolog plates, were exhibited by the soil bacterial communities associated with the three alfalfa genotypes, and those for the lignin peroxidase plants were the most unique. Significantly higher population levels of culturable, aerobic spore-forming and cellulose-utilizing bacteria, lower activity of the soil enzymes dehydrogenase and alkaline phosphatase, and higher soil pH levels, were also associated with the lignin peroxidase transgenic plants. Significantly higher population levels of culturable, aerobic spore-forming bacteria were also measured in the treatments containing the recombinant RMBPC-2 S. meliloti. 4. Population levels of protozoa, nematodes and micro-arthropods, DNA fingerprints of indigenous soil bacteria, and rates of microbial substrate-induced respiration were not significantly affected by the transgenic alfalfa and recombinant S. meliloti treatments. 5. These results suggest that the genetically engineered organisms caused detectable changes in some components of the soil ecosystem. The primary effects we observed were associated with the transgenic lignin peroxidase alfalfa and included alterations in plant growth and chemistry and changes in soil chemistry and microbiology.
Comparison of Thromboelastography and Conventional Coagulation Tests in Patients With Severe Liver Disease

Objective: Thromboelastography (TEG) may provide rapid and clinically important coagulation information in acutely ill patients with chronic liver disease (CLD). Our objective was to describe the relationship between TEG and conventional coagulation tests (CCTs), which has not been previously explored in this population. Methods: In acutely ill patients with severe CLD (Child-Pugh score > 9, category C), we conducted a prospective observational study investigating coagulation assessment as measured by both CCTs and TEG. We used quantile regression to explore 30 associations between TEG parameters and corresponding CCTs. We compared TEG and CCT measures of coagulation initiation, clot formation, clot strength, and fibrinolysis. Results: We studied 34 patients on a total of 109 occasions. We observed inconsistent associations between TEG and CCT measures of coagulation initiation: TEG (citrated kaolin [CK] assay) standard reaction time and international normalized ratio: R 2 = 0.117 (P = .044). Conversely, there were strong and consistent associations between tests of clot formation: TEG (CK) kinetics time and fibrinogen: R 2 = 0.202 (P < .0001) and TEG (CK) α angle and fibrinogen 0.263 (P < .0001). We also observed strong associations between tests of clot strength, specifically TEG MA and conventional fibrinogen levels, across all TEG assays: MA (CK) and fibrinogen: R 2 = 0.485 (P < .0001). There were no associations between TEG and D-dimer levels. Conclusions: In acutely ill patients with CLD, there are strong and consistent associations between TEG measures of clot formation and clot strength and conventional fibrinogen levels. There are weak and/or inconsistent associations between TEG and all other conventional measures of coagulation.
Early paleolithic of China and eastern Asia

In attempting to understand the course of human evolution and the nature of hominid adaptation over the past few million years, it is necessary to consider prevailing evidence from all parts of the world. Eastern Asia provides a range of important questions and challenges with regard to this evolutionary puzzle. Although evidence for earlier ape evolution is present in China (for example, at Lufeng in Yunnan Province), the earliest evidence for hominid presence appears to be in the Early Pleistocene, apparently the result of a migration of hominids to and subsequent adaptation within Eastern Asia. The archeological record provides a closer look at some technological aspects of this adaptation during the Early and Middle Pleistocene, showing both distinctive contrasts and intriguing continuities relative to the rest of the Old World.
HEREDITARY DEFECTS AND CONSERVATION GENETIC MANAGEMENT OF CAPTIVE POPULATIONS

The occurrence of hereditary disorders in conservation breeding programs may severely hamper the overall aim of such programs. The obstacles that arise in this context and the particular management strategies needed to deal with the problems are yet to be adequately addressed. Results from a literature review indicate that hereditary disorders may be fairly common in zoo populations. An example with albinism in a captive brown bear population bred in Nordic zoos is presented. It is demonstrated that the segregation pattern is consistent with an autosomal recessive allele, and carrier probabilities of live animals indicate that the allele occurs in high frequency in the present population. Removing animals with a probability of carrying the allele will result in loss of founder alleles considered particularly valuable. Zoo Biol 18:81–99, 1999. © 1999 Wiley-Liss, Inc.
Personalising Exergames for the Physical Rehabilitation of Children Affected by Spine Pain

Injuries or illnesses related to the lumbar spine need great clinical care as they are one of the most prevalent medical conditions worldwide. The use of exergames has been widespread in recent years and they have been put forward as a possible solution for motivating patients to perform rehabilitation exercises. However, both customizing and creating them is still a task that requires considerable investment both in time and effort. In this project we present a language with which we have designed a system based on the physical rehabilitation of patients suffering from bone-marrow injuries, which enables customization and generation of exergames. To assess the system, we have designed an experiment with an exergame based on the physical rehabilitation of the lumbar spine. The purpose of this was to assess its understanding and suitability, whose result reveals that the tool is fun, interesting and easy to use. It is hoped that this approach can be used to considerably reduce the complexity of creating new exergames, as well as supporting the physical rehabilitation process of patients with lower back pain.
Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus). We first assembled a 490‐Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large data set of genome‐wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8 million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large Ne and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype–environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.
How to Better Form Software Development Teams? An Analysis of Different Formation Criteria

In the competitive world of the on-demand software development market, some practices that increase companies' chances of delivering better results turn out to be an essential differentiator. Several studies in the literature discuss numerous criteria used by companies in the formation of teams. This research aims to analyze the criteria and factors in the formation of software teams and their impacts on the value perceived by the customer of the deliveries. We collected 31 project results scores of an R&D organization and performed a quantitative analysis comparing teams formed using two selection criteria: self-selection versus leader selection. We observed a statistical significance in the comparison between the selection criteria when tested with the longevity factor. Our results indicated that the self-selection team formation criteria had impact on value delivered to the customer. We also noticed this impact when, besides being self-selected, the team was also long-lived.
NAD metabolism in aging and cancer

NAD+ and its derivatives NADH, NADP+, and NADPH are essential cofactors in redox reactions and electron transport pathways. NAD serves also as substrate for an extensive series of regulatory enzymes including cyclic ADP-ribose hydrolases, mono(ADP-ribosyl)transferases, poly(ADP-ribose) polymerases, and sirtuin deacetylases which are O-acetyl-ADP-ribosyltransferases. As a result of the numerous and diverse enzymes that utilize NAD as well as depend on its synthesis and concentration, significant interest has developed in its role in a variety of physiologic and pathologic processes, and therapeutic initiatives have focused both on augmenting its levels as well as inhibiting some of its pathways. In this article, we examine the biosynthesis of NAD, metabolic processes in which it is involved, and its role in aging, cancer, and other age-associated comorbidities including neurodegenerative, cardiovascular, and metabolic disorders. Therapeutic interventions to augment and/or inhibit these processes are also discussed. Impact statement NAD is a central metabolite connecting energy balance and organismal growth with genomic integrity and function. It is involved in the development of malignancy and has a regulatory role in the aging process. These processes are mediated by a diverse series of enzymes whose common focus is either NAD’s biosynthesis or its utilization as a redox cofactor or enzyme substrate. These enzymes include dehydrogenases, cyclic ADP-ribose hydrolases, mono(ADP-ribosyl)transferases, poly(ADP-ribose) polymerases, and sirtuin deacetylases. This article describes the manifold pathways that comprise NAD metabolism and promotes an increased awareness of how perturbations in these systems may be important in disease prevention and/or progression.
Retrospective study on imported schistosomiasis in Morocco between 2005 and 2017

Since 2004, no indigenous cases of schistosomiasis have been found in Morocco; only imported cases have been detected. The aim of the present study was to describe and analyse the epidemiological profile of imported schistosomiasis between 2005 and 2017, and, by this, attract attention to the probability of a reintroduction of this disease. During this period, 27 cases were recorded in Morocco, with a male predominance (13:1). All cases reported were found among African immigrants from Mauritania (37%), Mali (18%) and Senegal (15%). Schistosoma heamatobium was the most dominant specie. Most cases were reported in Rabat and Agadir, where there are many snail habitats. To prevent a re-emergence of the disease, the main challenge would be to consolidate and maintain a sustainable surveillance and control system of the importation of bilharzia. The frequency of asymptomatic schistosomiasis justifies a systematic health check-up for all travellers, migrants and immigrants.
L’aspirine, les cyclo-oxygénases et les effets cardiovasculaires délétères de l’angiotensine II : Rôle des cyclo-oxygénases dans les effets de l’angiotensine II

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How Machine Learning Has Been Applied in Software Engineering?

Machine Learning (ML) environments are composed of a set of techniques and tools, which can help in solving problems in a diversity of areas, including Software Engineering (SE). However, due to a large number of possible configurations, it is a challenge to select the ML environment to be used for a specific SE domain issue. Helping software engineers choose the most suitable ML environment according to their needs would be very helpful. For instance, it is possible to automate software tests using ML models, where the model learns software behavior and predicts possible problems in the code. In this paper, we present a mapping study that categorizes the ML techniques and tools reported as useful to solve SE domain issues. We found that the most used algorithm is Naïve Bayes and that WEKA is the tool most SE researchers use to perform ML experiments related to SE. We also identified that most papers use ML to solve problems related to SE quality. We propose a categorization of the ML techniques and tools that are applied in SE problem solving, linking with the SWEBOK knowledge areas. In this Technical Report, we presents the complete references of all 177 selected publications.
p38 and STAT3 activation by vGPCR in KSHV-infected cells

Correspondence: Mingli Liu Department of Microbiology, Immunology and Biochemistry, Morehouse School of Medicine, 720 Westview Drive SW, Atlanta, GA 30310, USA Tel +1 404 752 1850 Fax +1 404 752 1179 Email mliu@msm.edu Abstract: The molecular mechanism whereby viral G protein-coupled receptor (vGPCR) signaling regulates vascular endothelial growth factor (VEGF) expression in Kaposi sarcoma (KS) formation remains incompletely defined. mECK36 cells, generated by transfection of mouse bone marrow endothelial cells with Kaposi’s sarcoma-associated herpesviruses (KSHV) bacterial artificial chromosome (KSHVBac36), have been reported to be angiogenic, tumorigenic, and suitable for demonstrating a nonredundant role for vGPCR in KSHV-mediated tumorigenesis. In this report we used mECK36 and the cells composed of wild-type KSHVBac36 or the cells without vGPCR, namely vGPCR-null KSHVBac36 mutant, to dissect the molecular mechanisms of VEGF secretion induced by vGPCR in the context of KSHV infection. We found that vGPCR activates VEGF transcription via p38 MAPK and STAT3 in mECK36 and mECK36-derived cell models. We also found that in cells containing KSHV genome, STAT3 is tyrosine-phosphorylated and translocated into the nucleus, transactivating the target VEGF gene by binding to the specific DNA element TT (N 4–5 ) AA in a strictly vGPCR-dependent manner. Moreover, treatment of mECK36-derived cells with AG490 or a dominant negative STAT3 DNA vector showed strong inhibitory effects on vGPCR-induced VEGF promoter activity. In addition, vGPCR can upregulate STAT3 mRNA levels. Taken together, our findings show that vGPCR plays a nonredundant role in STAT3 activation in KSHV infected cells and that this activation plays an important role in the connection of the viral oncogene vGPCR and VEGF upregulation. Our results indicate the broad signaling activating capacity of vGPCR in the context of KSHV infection and suggest that the STAT3 pathway could be targeted for preventing KSHV-mediated angiogenesis in KS.
Repercussions on sarcomeres of the myotendinous junction and the myofibrillar type adaptations in response to different trainings on vertical ladder

The myofibrillary types establish to the skeletal muscle functional and adaptive properties that influence the sarcomeric arrangement during muscle contraction and may have repercussions on an important related force transmission region of the locomotor apparatus, the myotendinous junction (MTJ). This study aimed to describe changes in myofibrillary type and sarcomeric lengths in the belly muscle and MTJ of the soleus and plantaris muscles associated with training protocols in vertical ladder. Thirty adults male Wistar rats were divided into three groups (n = 10): Control (CTR), No‐load Training (NLT), and Load Training (LT). Morphoquantitative analysis of different fibers types and sarcomere lengths were performed in distinct regions of plantaris and soleus muscles. In the plantaris muscle with both trainings, there was an increase in the cross‐sectional area (CSA) in Type I and II fibers (p < .0001) while sarcomeric lengths revealed greater lengths in the proximal and distal sarcomeres of NLT, although in the LT we found greater lengths in the belly and MTJ sarcomeres. The soleus muscle showed an increase in CSA muscle fiber only in the NLT (p < .0001) and revealed alterations in belly and MTJ sarcomere lengths with training. We concluded that plantaris muscle has an adaptive effect directly associated with training load, with hypertrophy in both trainings and sarcomere length inverse from belly and MTJ, in LT associated with increased force generation and transmission at the MTJ, although soleus muscle has a lower adaptive response to training stimuli with variation in the belly and distal sarcomere of the MTJ.
Online Automatic Characteristics Discovery of Faulty Application Transactions in the Cloud

Performance debugging and fault isolation in distributed cloud applications is difficult and complex. Existing Application Performance Management (APM) solutions allow manual investigation across a huge space of metrics, topology, functions, service calls, attributes and values a frustrating resource and time demanding task. It would be beneficial if one could gain explainable insights about a faulty transaction whether due to an error or performance degradation, such as specific attributes and/or url patterns that are correlated with the problem and can characterize it. Yet, this is a challenging task as demanding resources of storage, memory and processing are required and insights are expected to be discovered as soon as the problem occurs. As cloud resources are limited and expensive, supporting a large number of applications having many transaction types is impractical. We present Perceptor – an Online Automatic Characteristics Discovery of Faulty Application Transactions in the Cloud. Perceptor discerns attributes and/or values correlated with transaction error or performance degradation events. It does so with minimal resource consumption by using sketch structures and performs in streaming mode. Over an extensive set of experiments in the cloud, with various applications and transactions, Perceptor discovered non-trivial relevant fault properties validated by an expert.
Resting stage density and hatching of two cladoceran species from small ephemeral waters

We investigated resting stage densities of two cladocerans, Daphnia obtusa and Moina macrocopa, in very small and ephemeral water bodies (temperate zone rain puddles) and tested whether these species exhibit a prolonged diapause in such an environment. Densities of ephippia as well as resting eggs in puddles ranged between 10 2 and 10 4 per m 2 , and varied substantially within as well as among puddles. We determined the hatching success and temporal dynamics for resting stages collected from natural habitats and incubated at 15 °C with a 14L:10D light regime. Hatching success of both species was high (> 80 %) and steady, with new hatchlings appearing mostly within 3-8 days. M. macrocopa hatched significantly faster and slightly more successfully than D. obtusa. Decapsulation of D. obtusa ephippia had no effect on the hatching success but slowed down the hatching dynamics. Hatching of egg pairs from the same ephippium was mostly synchronised - in only less than 10 % of cases one egg hatched and the other remained potentially viable for the next flooding event. We compare our results with available data on cladoceran resting egg densities and hatching success, and discuss the possible causes of the high and steady hatching proportion of puddle cladocerans. A physiologically-based bet-hedging strategy may not be necessary if only a certain proportion of eggs are exposed to hatching cues or when the hydroperiod of temporary waters is longer than the cladoceran life cycle. Additionally, frequent destruction of localities may promote instantaneous termination of diapause even in ephemeral habitats such as puddles.