Miracle-dz/UniFAR-FTUs huggingface dataset:
Ant community composition and functional traits in newly established grasslands within agricultural landscapes

1. Ongoing intensification and fragmentation of European agricultural landscapes dramatically reduce biodiversity and associated functions. To sustain ecosystem services such as ant mediated pest control, the enhancement of perennial non-crop areas holds great potential. 2. To study the potential of newly established grasslands to enhance ant diversity and associated functions, we used hand collection data to investigate differences in ant community composition (a) between cereal crops, old grasslands, and new grassland transects of three years age; (b) depending on ant functional traits; and linked to (c) natural pest control services quantified through predation experiments. 3. Ant species richness did not significantly differ between new and old grasslands, but was significantly higher in grasslands compared to cereal crops. Contrary, ant community composition of new grasslands was more similar to cereal crops and distinct from the species-pool of old grasslands. The functional trait space covered by the ant communities overlapped between old and new grasslands but was extended in the old grasslands. Pest control did not differ significantly between habitat types, and therefore could not be linked to the prevalence of functional traits related to biocontrol services in new grasslands. 4. Our findings show trends of convergence between old and new grasslands, but also indicate that enhancing ant diversity through newly established grasslands takes longer than three years to provide comparable biodiversity and functions. 5. Synthesis and applications Newly established grasslands can increase ant species richness, abundance, and pest control in agroecosystems. However, three years after establishment, new grasslands were still dominated by common agrobiont ant species and lacked habitat specialists present in old grasslands, who require a constant supply of food resources and long colonization times. New grasslands represent a promising measure for enhancing agricultural landscapes but must be preserved in the longer term to sustain biodiversity and associated ecosystem services.
ScaR—a tool for sensitive detection of known fusion transcripts: establishing prevalence of fusions in testicular germ cell tumors

Bioinformatics tools for fusion transcript detection from RNA-sequencing data are in general developed for identification of novel fusions, which demands a high number of supporting reads and strict filters to avoid false discoveries. As our knowledge of bona-fide fusion genes becomes more saturated, there is a need to establish their prevalence with high sensitivity. We present ScaR, a tool that uses a scaffold realignment approach for sensitive fusion detection in RNA-seq data. ScaR detects a set of 50 synthetic fusion transcripts from simulated data at a higher sensitivity compared to established fusion finders. Applied to fusion transcripts potentially involved in testicular germ cell tumors (TGCTs), ScaR detects the fusions RCC1-ABHD12B and CLEC6A-CLEC4D in 9% and 28% of 150 TGCTs, respectively. The fusions were not detected in any of 198 normal testis tissues. Thus, we demonstrate high prevalence of RCC1-ABHD12B and CLEC6A-CLEC4D in TGCTs, and their cancer specific features. Further, we find that RCC1-ABHD12B and CLEC6A-CLEC4D are predominantly expressed in the seminoma and embryonal carcinoma histological subtypes of TGCTs, respectively. In conclusion, ScaR is useful for establishing the frequency of known fusion transcripts in larger data sets and detecting clinically relevant fusion transcripts with high sensitivity. Availability https://github.com/senzhaocode/ScaR
Design Principles for Bispecific IgGs, Opportunities and Pitfalls of Artificial Disulfide Bonds

Bispecific antibodies (bsAbs) are antibodies with two binding sites directed at different antigens, enabling therapeutic strategies not achievable with conventional monoclonal antibodies (mAbs). Since bispecific antibodies are regarded as promising therapeutic agents, many different bispecific design modalities have been evaluated, but as many of them are small recombinant fragments, their utility could be limited. For some therapeutic applications, full-size IgGs may be the optimal format. Two challenges should be met to make bispecific IgGs; one is that each heavy chain will only pair with the heavy chain of the second specificity and that homodimerization be prevented. The second is that each heavy chain will only pair with the light chain of its own specificity and not with the light chain of the second specificity. The first solution to the first criterion (knobs into holes, KIH) was presented in 1996 by Paul Carter’s group from Genentech. Additional solutions were presented later on. However, until recently, out of >120 published bsAb formats, only a handful of solutions for the second criterion that make it possible to produce a bispecific IgG by a single expressing cell were suggested. We present a solution for the second challenge—correct pairing of heavy and light chains of bispecific IgGs; an engineered (artificial) disulfide bond between the antibodies’ variable domains that asymmetrically replaces the natural disulfide bond between CH1 and CL. We name antibodies produced according to this design “BIClonals”. Bispecific IgGs where the artificial disulfide bond is placed in the CH1-CL interface are also presented. Briefly, we found that an artificial disulfide bond between VH position 44 to VL position 100 provides for effective and correct H–L chain pairing while also preventing the formation of wrong H–L chain pairs. When the artificial disulfide bond links the CH1 with the CL domain, effective H–L chain pairing also occurs, but in some cases, wrong H–L pairing is not totally prevented. We conclude that H–L chain pairing seems to be driven by VH–VL interfacial interactions that differ between different antibodies, hence, there is no single optimal solution for effective and precise assembly of bispecific IgGs, making it necessary to carefully evaluate the optimal solution for each new antibody.
Interactions among trees: A key element in the stabilising effect of species diversity on forest growth

Species diversity (hereafter diversity) is a major driver of ecosystems functioning (Cardinale et al., 2012; Hooper et al., 2012). In particu‐ lar, there is mounting evidence that diversity stabilises forest growth under fluctuating environmental conditions (Aussenac et al., 2017; Hutchison, Gravel, Guichard, & Potvin, 2018; Jucker, Bouriaud, Avacaritei, & Coomes, 2014; Morin, Fahse, Mazancourt, Scherer‐ Lorenzen, & Bugmann, 2014; Río et al., 2017). However, although significant progress has been made in recent years, our understand‐ ing of the mechanisms underlying the diversity–stability relationship in forest ecosystems remains incomplete. Different theories stand in opposition as regards the link be‐ tween diversity and stability. On the one hand, the insurance hypothesis predicts that diversity stabilises the productivity of com‐ munities (Mazancourt et al., 2013; Yachi & Loreau, 1999) because species differences in their response to fluctuating environmental conditions generate some growth asynchrony, which enables com‐ pensations among them and thereby stabilises the community‐level productivity. This theory does not account, however, for the way interspecific interactions impact community dynamics. On the other hand, May's (1973) theory and further developments (see the re‐ view in Tang and Allesina (2014)) and a test of theory in Jacquet et al. (2016) predict that diversity destabilises community dynamics Received: 30 June 2018 | Accepted: 20 November 2018 DOI: 10.1111/1365‐2435.13257
Motor Skills in the Structure of Physical Fitness of 7-Year-Old Boys

The purpose of this study was to determine the weight of motor skills in the structure of motor fitness of 7-year-old boys. Materials and methods. The study participants were 38 7-year-old boys. The children and their parents were informed about all the features of the study and gave their consent to participate in the experiment. The research methods used in the study include analysis of scientific and methodological literature, pedagogical observations, testing of motor fitness, probabilistic approach to assessing the learning process, methods of mathematical statistics. Results. The level of fitness of the 7-year-old boys is homogeneous by the development of “agility” and “movement coordination”, inhomogeneous – by the development of arm strength and vestibular stability. The 7-year-old boys’ motor fitness is determined by their physical development, the level of general physical fitness and the level of motor skills development. A graphic representation of a two-factor model of testing results shows that analysis identifies two sets of data with high correlation coefficients. The first set includes tests No. 2, 1, 4, and 5, which characterize physical development, agility and endurance; the second – the level of proficiency in exercises No. 14, 13, 12, and the result of test No. 7 “Mixed hang rope pull-ups”. Conclusions. Based on factor analysis, the study found that the level of proficiency in exercises determines the variation of testing results by 28.437%, and the development of motor skills is a priority in the educational process at primary school. The development of “agility” and “movement coordination” ensures the formation of motor skills, and the development of arm strength and vestibular stability is the reserve in training boys aged 7 which will make it possible to increase the effectiveness of the educational process.
Genetic diversity of rhizobia and plant growth promoting rhizobacteria of soil under the influence of Piliostigma reticulatum (DC.) Hochst and their impact on shrub growth

Piliostigma reticulatum shrub is a native legume found in fallow areas in dry and semi-dry savanna soil and is used in intercropping systems. The aim was to understand the functioning of the rhizosphere, particularly the involvement of symbiotic and free living-N fixing bacteria. Soil extracts collected from P. reticulatum roots were sampled in two contrasting areas and endophytic bacterial communities were isolated using three trap host species (F. albida, A. bivenosa and V. seyal). Potential endophytic bacteria (PEB) were characterized by RFLP, nifH PCR and by 16S rRNA gene sequencing. The subsequent behavior of P. reticulatum was monitored in vitro by measuring leaf weight, biomass and chlorophyll content, after inoculation with PEB. This approach enabled isolation of 59 bacteria belonging to different genotypes. The most abundant genera were Cohnella (27.65%) among which 11 isolates clustered together and could represent a new species closely related to C. plantaginis. The other dominant genera were Paenibacillus (21.27%), Bradyrhizobium (14.89%) and Ensifer (8.5%). The nitrogen fixing gene (nifH) was detected in 21 strains and in particular, detected in a single isolate (PZS_S04) close to Cohnella xylanilytica. The strains PZS_S05 (Ensifer) and PZG_A18 (Cohnella) significantly increased certain parameters including shoot dry weight, shrub height at 90 days and photosynthetic activity (SPAD), compared to non-inoculated controls.The result obtained showed that soil under the influence of P. reticulatum roots harbored a specific diversity of endophytic bacteria including two free living-N fixing bacteria with the potential to improve the growth of P. reticulatum in natural conditions. Key words: Piliostigma reticulatum, microbiology, phylogeny, Potential endophytic bacteria (PEB), nitrogen-fixing bacteria.
Hoarding Bad News: When Non-financial Firms Hold Financial Assets

This paper theoretically illustrates and empirically examines how listed non-financial firms use financial assets as an earnings manipulation tool with bad-news-hoarding motives. China created its first accounting standards for financial instruments in 2007, which classify financial assets based on the highly subjective “managerial holding intention” criterion, and financial assets accounted by fair value methods can affect current profits and losses. We find that during the years 2007 through 2016, financial asset holding is positively associated with the likelihood of stock price crashes for Chinese listed firms. The effect is more pronounced for firms with a CEO from a finance background, high information asymmetries, and weak governance. In addition, we identify accrual earnings management as a channel through which financial asset holding increases stock price crash risk. Our evidence indicates that in typical emerging markets such as China, fair value accounting may have unintended consequences, inducing non-financial firms to employ financial assets as a tool to hoard bad news.
Survival Analysis of Patients With High Blood Pressure Until Acute Renal Failure in the SPRINT Study

Background: High blood pressure (HBP) is one of the most prevalent diseases which has affected many people in different societies. It is also the cause of several other chronic and fatal diseases. Acute renal failure (ARF) represents an independent risk factor for morbidity, resulting in a prolonged period of hospitalization of the survived patients. Thus, survival analysis of the patients with HBP until ARF and determination of the associated factors are of utmost significance. Materials and Methods: The current research examined the survival of patients with HBP until ARF using the Weibull model. We obtained the data from Systolic Blood Pressure Intervention Trial (SPRINT). The studied population included patients with systolic blood pressure (SBP of 130-180 mm Hg). The follow-up median was 3.26 years in our study. Results: Out of a total of 842 patients, 590 subjects (70.1%) were male and 252 subjects (29.9%) were female. Moreover, from these 842 patients, 85 (4.5%) died of cardiovascular diseases, 298 (15.7%) were diagnosed with ARF, and 459 (54.5%) were censored. According to the outcomes of the Weibull model of competing risks, the indexes of gender, albumin/creatinine ratio in urine, glomerular filtration rate, and being in the category of patients with chronic kidney disease (CKD) were effective factors associated with the survival of patients. Conclusion: According to the outcomes of this study, controlling blood pressure can greatly reduce the incidence of kidney failure.
Butterfly assemblages from Amazonian flooded forests are not more species-poor than from unflooded forests

The Amazonian flooded and upland forests harbour distinct assemblages of most taxonomic groups. These differences can be mainly attributed to flooding, which may affect directly or indirectly the persistence of species. Here, we compare the density, richness and composition of butterfly assemblages in vaórzea and terra firme forests, and evaluate whether terrain elevation and flooding can be used to predict the assemblage structure. We found that the total abundance and number of species per plot is higher in vaórzea than in terra firme forests. Vaórzea assemblages showed a higher dominance of abundant species than terra firme assemblages, in which low-flying Haeterini butterflies had higher abundance. After standardizing species richness by sample size and/or coverage, species richness estimates for vaórzea and terra firme forests were similar. There was strong turnover in species composition across vaórzea and terra firme forests associated with terrain elevation, most likely due to differences in the duration of flooding. Despite a smaller total area, less defined vegetation strata, more frequent disturbances and the younger geological age of floodplain forests, Nymphalid butterfly assemblages are not more species poor there than in unflooded forests.
Histological studies of the pheromone-producing gland in female of Spodoptera littoralis (Lepidoptera: Noctuidae)

Sex pheromone gland in female Spodoptera littoralis was studied histologically. The scent gland is located in the body cavity beneath the 7 and 8 abdominal tergites and ventrally around the ninth segments. The gland lies in the body cavity has an eversible sac forming a ring shaped structure. The eversible sac lined with cuticular layer that has spines pointing toward the lumen of the sac. The gland composed of two distinct regions secretory and storing. Cells of each region are composed of a single layer of flattened, columnar or cuboidal epithelial cells containing large circular or oval basal located nuclei and a layer of cuticle covering the epithelial cells with distinct spines. PAS-positive substances were demonstrated intracellular for both regions. In addition, the leuminal contents within the storing region are intensely PAS stained. Transmission electron microscopy of the ventral surface of the 9 segment showed the presence of electron opaque spherical bodies in the epithelial cells.
Immediate Dentoalveolar Restoration in Compromised Sockets: Technique and Bone Biology

The aim of this chapter is to describe a one-stage technique called immediate dento- alveolar restoration (IDR) which uses autogenous bone graft harvested from maxillary tuberosity in order to restore bone defects in compromised alveolar sockets and also to achieve soft tissue stability along the years. The IDR is a flapless surgical and prosthetic technique established to broaden indications for immediate loading on individual teeth. In this way, tissue loss with varied extensions are reconstructed in the same surgical session as implant placement and provisional crown installation, reducing the number of interventions and retaining esthetic predictability. Successful esthetic and functional outcomes and reestablishment of the alveolar process after bone reconstruction were observed during the follow-up period. The predictable results and soft tissue stability can be achieved following the IDR protocol.
Physics comics learning media based on Engklek traditional games on parabolic motion topics to improve creativity

In the 21st century science education starts to need innovation and is considered to bring about science, technology, engineering, mathematics (STEM) to provide the context learned in learning. Comic strips have been around for more than one hundred years. Comics become an interesting medium in the learning process as a global phenomenon. Comics are not only as a medium of entertainment but can be utilized in the field of education in schools. The aim of this study is to examine the effect of the use of comic media on the development of students' creativity in teaching the subject of parabolic movement in physics lesson. This research method is the R & D Educational Development (Educational Research and Development) with the 4-D model consists of 3 stages, i.e.: define, design, and develop. The physics teachers and peer reviewers are to assess and review the product from the theory feasibility and presentation of the media. The media accepts assessments and inputs for use as media improvements. The trial uses assessment tests (question test) and non-tests (questionnaire) to students. The result this research is physics comics learning media based on Engklek traditional games in the parabola motion topics to improve creativity can disseminate to students for physics learning process outside and inside the school.
Assessment of burnout among primary teachers in confinement during the COVID-19 period in Morocco: case of the Kenitra

Introduction Confinement, because of the COVID-19 pandemic, could have problems on the mental health of the population. Teachers responsible for giving distance courses during this period could be psychologically stressed. The aim is to assess the magnitude results of burnout and associated factors among primary school teachers in Kenitra in Morocco during this confinement period. Methods This is a cross-sectional study, which was conducted during the two months of April and May 2020. Burnout was evaluated by the Maslach Burnout Inventory MBI with 16 items, specific to the context of Moroccan teachers and the factors of stress were assessed using a questionnaire developed by the research team. We used the Chi-square test to determine the association between two qualitative variables anda logistic regression for an overall statistical analysis. Results The average age was 38.6 ± 9.9 years. The MBI revealed that 68 teachers (54%) were victims of burnout, of which 47 (38%) had a low level; 15 (12%) had a moderate level and six (5%) had a severe burnout. Logistic regression analysis has shown that the risk factors for burnout during this confinement period are: the use and development of skills in new information and communication technologies (p<0,05); work/family conflict (p<0,05); social support (p<0,05); and the workload related to distance education (p≤0,05). Conclusion In light of these results, interventions aimed at promoting mental well-being teachers during and after confinement should be implemented immediately.
Transfer of Xanthomonas campestris pv. arecae, and Xanthomonas campestris pv. musacearum to Xanthomonas vasicola (Vauterin) as Xanthomonas vasicola pv. arecae comb. nov., and Xanthomonas vasicola pv. musacearum comb. nov. and description of Xanthomonas vasicola pv. vasculorum pv. nov.

Recent DNA sequence and other data indicated that several important bacterial pathogens should be transferred into the species Xanthomonas vasicola Vauterin 1995. The first objective of this letter is to propose the transfer of X. campestris pv. musacearum (Yirgou and Bradbury 1968) Dye 1978 to X. vasicola Vauterin 1995. The second objective is to give a clear overview of the different evolutionary lineages that constitute the species X. vasicola, in the light of recent genomics analyses. These analyses also indicate that strains described as [X. campestris pv. zeae] (Qhobela, Claflin, and Nowell 1990; Coutinho and Wallis 1991) fall within the species X. vasicola Vauterin 1995. Furthermore, the sequence of its gyrB gene suggested that X. campestris pv. arecae (Rao and Mohan 1970) Dye 1978 is closely related to the type strain of X. vasicola. Note that in this manuscript pathovar names that have no valid standing in nomenclature are presented with square brackets as is standard.
Effets de densite et de temperature sur les ions des plasmas denses et chauds : structure atomique dans un modele multiconfigurationnel, equilibre statistique

Etude des effets dus a l'environnement sur la structure quantique d'un ion dans un plasma dense et chaud type plasma de fusion laser. Les proprietes atomiques sont calculees pour chaque degre d'ionisation en incluant les interactions de configurations. On analyse leurs variations en fonction de la densite electronique locale et on met en evidence les phenomenes d'abaissement du continu, d'ionisation par pression, d'elargissement de raies et de deplacement par polarisation du plasma. Calcul des populations des divers etats des divers degres d'ionisation, dans l'hypothese de l'e. T. L. Etude des influences croisees de la temperature et de la densite electronique moyenne sur les populations