Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved meiotic mechanisms in the cnidarian Clytia hemisphaerica revealed by Spo11 knockout

During meiosis, DNA recombination allows the shuffling of genetic information between the maternal and paternal chromosomes. Recombination is initiated by double strand breaks (DSBs) catalyzed by the conserved enzyme Spo11. How this crucial event is connected to other meiotic processes is surprisingly variable depending on the species. Here, we knocked down Spo11 by CRISPR in the jellyfish Clytia hemisphaerica, belonging to Cnidaria, the sister group to Bilateria (where classical animal models are found). Spo11 mutants fail to assemble synaptonemal complexes and chiasmata, and in consequence homologous chromosome pairs disperse during oocyte growth, creating aneuploid but fertilizable eggs that develop into viable larvae. Clytia thus shares an ancient eukaryotic dependence of synapsis and chromosome segregation on Spo11-generated DSBs, and provides new evolutionary perspectives on meiosis regulation.
The conversion of the two-carbon acetyl-CoA to the twenty-seven-carbon, tetracyclic cholesterol via the meval-

Journal of Lipid Research Volume 60, 2019 1643 Copyright © 2019 Coates and Brown. Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc. The conversion of the two-carbon acetyl-CoA to the twenty-seven-carbon, tetracyclic cholesterol via the mevalonate pathway is a remarkable feat of anabolic engineering. Its earliest steps yield mevalonate, followed by isoprenoid precursors that condense to produce the squalene backbone of cholesterol (Fig. 1). Oxygenation and cyclization form the steroid nucleus, upon which the pathway bifurcates into two parallel branches, Bloch and KandutschRussell, each involving successive rounds of reduction and demethylation. Ultimately, the synthesis of a single cholesterol molecule expends approximately one hundred ATP equivalents and eleven oxygen molecules. It comes as no surprise, then, that the complexity of cholesterol synthesis is matched only by its exquisite regulation. During sterol excess, pathway flux is curtailed in the shortterm by accelerated degradation of the rate-limiting enzyme 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), which generates mevalonate, and in the long-term by inactivation of sterol regulatory element binding protein-2 (SREBP-2), a master transcriptional regulator that promotes cholesterol synthesis and uptake (1). In a classic example of feedback inhibition, cholesterol suppresses its own production by preventing the proteolytic cleavage and maturation of SREBP-2 (2). However, it does not induce HMGCR turnover (2). Indeed, since the pioneering work of Kandutsch and Chen over forty years ago, it has been understood that cholesterol is not the sole sterol regulating this pathway (3, 4). For instance, oxidized derivatives of cholesterol such as 25-hydroxycholesterol are potent inducers of both HMGCR degradation and SREBP-2 inactivation (5). Yet the contribution of mevalonate pathway intermediates to cholesterol homeostasis has remained elusive—and even controversial.
Physical Fitness and Performance in Talented & Untalented Young Chinese Soccer Players

Sports performance is a complex process that involves many factors, including ethnic and racial differences. China’s youth soccer is in a process of constant development, although information about the characteristics of its players and their methodological systems is scarce. The aim of this retrospective study was to characterize the physical fitness and the competitive performance of 722 Chinese players of three sports categories (8.0–9.9, 10.0–11.9 and 12.0–13.9 years), who were classified by their coaches as talented (n = 204) or untalented (n = 518). Players were assessed for anthropometry (body height, body mass, body mass index), lung capacity (Forced Vital Capacity), jumping performance (Squat Jump, Countermovement Jump and Abalakov tests), sprinting performance (10 m and 30 m Sprint tests), agility performance (Repeated Side-Step test) and flexibility (Sit & Reach test). A descriptive, comparative, correlational and multivariate analysis was performed. Competitive ranking was created in order to act as dependent variable in multiple linear regression analysis. Results indicate that Chinese players classified as talented have better motor performance than untalented ones. However, these differences are neither related nor determine the competitive performance of one group or the other.
Irrigation Intervals and Grazing Intensity Induced Variations in Growth and
Chemical Components of Periploca Angustifolia (Labill) Grown In North Sinai

Two field trials were conducted in the experimental farm of Baloza Research Station, located at North Sinai. The objective of this study was to evaluate the effects of irrigation intervals (2, 3 and 4 weeks) and cutting heights (30 and 60 cm above the ground surface) on growth parameters and chemical contents of Periploca angustifolia (Labill) plants. Obtained results indicated that most of growth parameters were decreased in response to various irrigation intervals. Carbohydrates, lipids and K contents (in leaves) were decreased due to irrigation intervals, while the reverse was observed in protein. On the other hand, carbohydrate and K contents in stems were increased as irrigation intervals increased while the reverse was true in protein, lipids and ash contents. No changes were found in various growth parameters with increasing cutting height from 30 to 60 cm except in plant dry weight in the first and second cut, fresh weight and leaf area in the second cut which were decreased with increasing cutting height. With increasing cutting height, carbohydrate was higher; nevertheless, protein and K were lower in leaves. In the opposite side, carbohydrate was lower while protein and lipids were higher at 60 cm cutting in stem.
Accuracy and Clinical Relevance of Intra-Tumoral Fusobacterium nucleatum Detection in Formalin-Fixed Paraffin-Embedded (FFPE) Tissue by Droplet Digital PCR (ddPCR) in Colorectal Cancer

The use of droplet digital PCR (ddPCR) to identify and quantify low-abundance targets is a significant advantage for accurately detecting potentially oncogenic bacteria. Fusobacterium nucleatum (Fn) is implicated in colorectal cancer (CRC) tumorigenesis and is becoming an important prognostic biomarker. We evaluated the detection accuracy and clinical relevance of Fn DNA by ddPCR in a molecularly characterized, formalin-fixed, paraffin-embedded (FFPE) CRC cohort previously analyzed by qPCR for Fn levels. Following a ddPCR assay optimization and an analytical evaluation, Fn DNA were measured in 139 CRC FFPE cases. The measures of accuracy for Fn status compared to the prior results generated by qPCR and the association with clinicopathological and molecular patients’ features were also evaluated. The ddPCR-based Fn assay was sensitive and specific to positive controls. Fn DNA were detected in 20.1% of cases and further classified as Fn-high and Fn-low/negative, according to the median amount of Fn DNA that were detected in all cases and associated with the patient’s worst prognosis. There was a low agreement between the Fn status determined by ddPCR and qPCR (Cohen’s Kappa = 0.210). Our findings show that ddPCR can detect and quantify Fn in FFPE tumor tissues and highlights its clinical relevance in Fn detection in a routine CRC setting.
Herpes simplex virus 1 expressing GFP-tagged virion host shutoff (vhs) protein uncouples the activities of degradation and nuclear retention of the infected cell transcriptome

Virion host shutoff (vhs) protein is an endoribonuclease encoded by herpes simplex virus 1 (HSV1). Vhs causes a number of changes to the infected cell environment that favour translation of late (L) virus proteins: cellular mRNAs are degraded, immediate-early (IE) and early (E) viral transcripts are sequestered in the nucleus with polyA binding protein (PABPC1), and dsRNA is degraded to help dampen the PKR-dependent stress response. To further our understanding of the cell biology of vhs, we constructed a virus expressing vhs tagged at its C-terminus with GFP. When first expressed, vhs-GFP localised to juxtanuclear clusters, and later it colocalised and interacted with its binding partner VP16, and was packaged into virions. Despite vhs-GFP maintaining activity when expressed in isolation, it failed to degrade mRNA or relocalise PABPC1 during infection, while viral transcript levels were similar to those seen for a vhs knockout virus. PKR phosphorylation was also enhanced in vhs-GFP infected cells, in line with a failure to degrade dsRNA. Nonetheless, mRNA FISH revealed that as in Wt but not Δvhs infection, IE and E, but not L transcripts were retained in the nucleus of vhs-GFP infected cells at late times. Moreover, a representative cellular transcript which is ordinarily highly susceptible to vhs degradation, was also retained in the nucleus. These results reveal that the vhs-induced nuclear retention of the infected cell transcriptome is dependent on vhs expression but not on its endoribonuclease activity, uncoupling these two functions of vhs. Importance Like many viruses, herpes simplex virus 1 (HSV1) expresses an endoribonuclease, the virion host shutoff (vhs) protein, which regulates the RNA environment of the infected cell and facilitates the classical cascade of virus protein translation. It does this by causing the degradation of some mRNA molecules and the nuclear retention of others. Here we describe a virus expressing vhs tagged at its C-terminus with green fluorescent protein (GFP) and show that the vhs-GFP fusion protein retains the physical properties of native vhs, but does not induce the degradation of mRNA. Nonetheless, vhs-GFP maintains the ability to trap the infected cell transcriptome in the nucleus, proving for the first time that mRNA degradation is not a prerequisite for vhs effects on the nuclear transcriptome. This virus has therefore uncoupled the nuclear retention and degradation activities of vhs, providing new understanding of vhs during infection.
Instrumentation of the Creative Economy Under the Theory U Concepts

The West Amazon peoples show a low economic and social development pattern, even when there are plenty of natural resources. It looks like there is a huge gap between these resources, the investments, the knowledge, and the public policies able to create a better life quality for the Amazonians. This work looks forward to promoting the development of the Amazon according to ways shown by the creative economy and the U Theory, special attention will be given to the Amazonian situation and the path to its cognitive development and subsequent economic development. The work is in the academia and communities that search for a viable alternative to creative and sustainable development. From this standpoint, the proposed general objective is to study the instrumentation of the creative economy with input from the U theory. As specific objectives: to perform a critical analysis of the raised concepts (1); to point towards the circularity elements of the creative economy in the community (2); and refer to the acknowledged instrumentation in this study in support to the creative economy, having as baseline the U Theory (3). Hence, the problem proposed is: how the concepts brought up by the creative economy with the support of the U Theory can contribute to the West Amazon’s economic, social and sustainable development promotion. It is meant as qualitative research with a content analysis method, in which the data was gathered through bibliographic search and interviews. In the results, it is proposed a competence and ability management space to the leaderships, beginning at the Amazonian home. It is due to capacitating and training these producers under innovation, entrepreneurship, and sustainability concepts. It is requested the attendance to rules and techniques be respected by the producer of products elaborated with the available raw material.
Second generation sparse models

Sparse data models, where data is assumed to be well represented as a linear combination of a few elements from a learned dictionary, have gained considerable attention in recent years, and their use has led to state-of-the-art results in many applications. The success of these models is largely attributed to two critical features: the use of sparsity as a robust mechanism for regularizing the linear coefficients that represent the data, and the flexibility provided by overcomplete dictionaries that are learned from the data. These features are controlled by two critical hyper-parameters: the desired sparsity of the coefficients, and the size of the dictionaries to be learned. However, lacking theoretical guidelines for selecting these critical parameters, applications based on sparse models often require hand-tuning and cross-validation to select them, for each application, and each data set. This can be both inefficient and ineffective. On the other hand, there are multiple scenarios in which imposing additional constraints to the produced representations, including the sparse codes and the dictionary itself, can result in further improvements. This thesis is about improving and/or extending current sparse models by addressing the two issues discussed above, providing the elements for a new generation of more powerful and flexible sparse models. First, we seek to gain a better understanding of sparse models as data modeling tools, so that critical parameters can be selected automatically, efficiently, and in a principled way. Secondly, we explore new sparse modeling formulations for effectively exploiting the prior information present in different scenarios. In order to achieve these goals, we combine ideas and tools from information theory, statistics, machine learning, and optimization theory. The theoretical contributions are complemented with applications in audio, image and video processing.
A Gentle Introduction to the RM2006 Methodology

We present the basic concepts used in market risk evaluations, as well as the standard methodologies to compute quantitatively the risk. A new methodology is introduced with the goal to incorporate the state-of-the-art knowledge about financial time series. The performance evaluation of risk methodologies is explained, and the performance measures of the main risk methodologies are compared. The presentation stays at the conceptual level and uses the minimum number of formula needed for clarity.
Motor Vehicle Crashes and Injuries Involving Teenage Drivers: Future Directions for Research

This circular includes a summary of the discussions by experts on teenage driving that took place at a 2008 meeting and workshop organized by the TRB Subcommittee on Young Drivers. The meeting and workshop were convened to identify research that is needed to answer the most critical and timely scientific questions about teenage drivers. During the meeting, full-group discussions were intermixed with smaller subgroup deliberations. Each of these sessions involved a particular goal for the participating groups. The intent of this structure was to elicit and discuss as many research-specific issues as the participants considered important for identifying needed research in the young driver field. Participants reviewed ways in which the teenage driver problem has been addressed, how approaches have developed and changed over time, and commented on the past and present status of research in this area. The context and state of existing knowledge led to the identification of the following areas of research as most critical: 1) advancing the science of teenage driving; 2) learning to drive safely: how competence develops; 3) teenage driving exposure issues; 4) parenting issues: how parents influence teenage driving; and 5) passenger issues: how passengers influence teenage driving and crash risk. Following the meeting, members of the planning committee developed potential research topics and specific items for suggested research in the five priority areas. The document is intended to provide both new and veteran researchers with a guide to research questions whose answers are of particular importance for efforts to reduce motor vehicle crashes, injuries, and deaths involving teenage drivers.
Wealth in the Utility Function

Wealth in the utility function (WIU) has been increasingly used in macroeconomic models and this specification can be justified by a few theories such as Max Weber’s (1904-05, German; 1958) theory on “spirit of capitalism. ” We incorporate the WIU into a general equilibrium consumption-portfolio choice model to study the implications of the WIU for consumption inequality, equilibrium interest rate, and equity premium—an unexplored area in the literature. Our general equilibrium framework features recursive exponential utility, uninsurable labor risks, and multiple assets and can deliver closed-form solutions to help disentangle the effects of the WIU in driving the key results. We show a stronger preference for wealth lowers the risk-free rate but increases the consumption inequality and equity premium in the equilibrium. We show these properties improve the model’s performance in explaining the data. We also compare the WIU with a closely related hypothesis, habit formation, and find that they have opposite effects on equilibrium asset returns and consumption inequality. JEL Classification Numbers: C61, D81, E21.
DEVELOPMENT OF TRUCK TRIP-GENERATION RATES BY GENERALIZED LAND-USE CATEGORIES

One method of truck trip-generation analysis--that is, the relation between the number of truck trips produced in or attracted to an area and the characteristics of that area--is land-area trip-rate analysis. This technique develops truck trip rates, usually on a per acre or per square mile basis, for each of the various land-use types in a study area. This study reviews previous research on land-area truck trip rates and develops additional land-area truck trip rates for several cast-study cities. Use of these rates may prove valuable in the analysis of the impact of major truck generating activities in localized sections of an urban area. An examination of the developed truck trip rates shows that, in general, commercial and industrial land uses are the largest generators of truck trips. Much variation is apparent, however; only residential land uses exhibit any consistency when the results of this research and previously reported truck trip rates are compared. (Author)
Plant peptidoglycan precursor biosynthesis: Conservation between moss chloroplasts and Gram-negative bacteria

An accumulation of evidence suggests that peptidoglycan, consistent with a bacterial cell wall, is synthesised around the chloroplasts of many photosynthetic eukaryotes, from glaucophyte algae to land plants at least as evolved as pteridophyte ferns, but the biosynthetic pathway has not been demonstrated. We employed mass spectrometry and enzymology in a twofold approach to characterize the synthesis of peptidoglycan in chloroplasts of the moss Physcomitrium (Physcomitrella) patens. To drive the accumulation of peptidoglycan pathway intermediates, P.patens was cultured with the antibiotics phosphomycin, D-cycloserine and carbenicillin, which inhibit key peptidoglycan pathway proteins in bacteria. Mass spectrometry of the TCA-extracted moss metabolome revealed elevated levels of five of the predicted intermediates from UDP-GlcNAc through to the UDP-MurNAc-D,L-diaminopimelate (DAP)-pentapeptide. Most Gram negative bacteria, including cyanobacteria, incorporate meso-diaminopimelate (D,L-DAP) into the third residue of the stem peptide of peptidoglycan, as opposed to L-lysine, typical of most Gram positive bacteria. To establish the specificity of D,L-DAP incorporation into the P.patens precursors, we analysed the recombinant protein, UDP-MurNAc-tripeptide ligase (MurE), from both P.patens and the cyanobacterium Anabaena sp. strain PCC 7120. Both ligases incorporated D,L-DAP in almost complete preference to L-Lys, consistent with the mass spectrophotometric data, with catalytic efficiencies similar to previously documented Gram negative bacterial MurE ligases. We discuss how these data accord with the conservation of active site residues common to DL-DAP-incorporating bacterial MurE ligases and of the probability of a horizontal gene transfer event within the plant peptidoglycan pathway.
Age‐related differences in AIS 3+ crash injury risk, types, causation and mechanisms

Data from the National Automotive Sampling System-Crashworthiness Data System (NASS-CDS) and the Crash Injury Research Engineering Network (CIREN) cases were analyzed to (1) define how occupant age affects crash exposure and the risk of AIS 3+ injury and (2) identify how age affects injury types and causation while considering comorbid factors and gender. Multivariate logistic regression models developed from NASS indicated that age significantly increases the risk of AIS 3+ injury to almost every body region in all crash modes. The largest age effect was observed for the thorax in frontal crashes and was modulated by gender such that older women were at significantly higher risk relative to younger women than were older men relative to younger men. A subset of 1289 CIREN cases, analyzed for injury causation, found occupants under age 25 and over 65 years sustained greater proportions of head and thoracic injuries respectively. For frontal crashes, thoracic injury type changed from soft to bony tissue injury as age increased and comorbid factors were more common for the older occupants. Crash severity was consistently lower for the older age groups and outcomes were worse in the older occupants even for similar crash severity and injury.
Comparison of Outcomes among Chronic Kidney Disease V Patients with COVID-19 at the National Kidney and Transplant Institute: A Retrospective Cohort Study

Background There is very little published data on outcomes of COVID-19 among chronic kidney disease (CKD) patients. We compared the outcomes of COVID-19 in a tertiary care renal hospital among CKD V patients on hemodialysis (HD), peritoneal dialysis (PD), and dialysis initiation, in terms of duration of hospitalization, in-patient mortality, and 30-day mortality. Methods A total of 436 CKD V patients, on either HD, PD, or dialysis initiation, with COVID-19 who were admitted at the National Kidney and Transplant Institute (NKTI) from March 13, 2020, to August 31, 2020, were included. Kaplan–Meier survival analysis was performed. Comparison of probability of mortality by group was performed using Log-Rank test. p values ≤0.05 were considered statistically significant. Results Among 436 CKD V patients, 298 (68%) were on HD, 103 (24%) were on PD, and 35 (8%) required dialysis initiation. Overall in-hospital mortality was 34%; 38% were on HD, 20% on PD, and 37% on dialysis initiation. Total 30-day mortality was 27%; 32% were on HD, 26% on PD, and 16% on dialysis initiation. Median follow-up was 24 days. Among the 137 deaths recorded, total median time to death was 10 days; 8.5 days, 15.5 days, and 9 days for HD, PD, and dialysis initiation groups, respectively. Probability of mortality was significantly higher in HD patients versus PD patients (p < 0.00001) and in the dialysis initiation group compared to PD patients (p=0.0234). Mortality probability, however, was not significantly different in HD patients versus the dialysis initiation group (p=0.63). Conclusion Among CKD V patients diagnosed with COVID-19 at the NKTI, those on HD and on dialysis initiation had significantly higher in-hospital and 30-day mortality, compared to patients on PD.