Miracle-dz/UniFAR-FTUs huggingface dataset:
The Numerics of Physical Parametrization in the ECMWF Model

The numerical aspects of physical parametrization are discussed mainly in the context of the ECMWF Integrated Forecasting System. Two time integration techniques are discussed. With parallel splitting the tendencies of all the parametrized processes are computed independently of each other. With sequential splitting, tendencies of the explicit processes are computed first and are used as input to the subsequent implicit fast process. It is argued that sequential splitting is better than parallel splitting for problems with multiple time scales, because a balance between processes is obtained during the time integration. It is shown that sequential splitting applied to boundary layer diffusion in the ECMWF model leads to much smaller time truncation errors than does parallel splitting. The so called Semi-Lagrangian Averaging of Physical Parametrizations (SLAVEPP), as implemented in the ECMWF model, is explained. The scheme reduces time truncation errors compared to standard first order methods, although a few implementation questions remain. In the scheme fast and slow processes are handled differently and it remains a research topic to find the optimal way of handling convection and clouds. Process specific numerical issues are discussed in the context of the ECMWF parametrization package. Examples are the non-linear stability problems in the vertical diffusion scheme, the stability related mass flux limit in the convection scheme and the fast processes in the cloud microphysics. Vertical resolution in the land surface scheme is inspired by the requirement to represent diurnal to annual time scales. Finally, a new coupling strategy between atmospheric models and land surface schemes is discussed. It allows for fully implicit coupling also for tiled land surface schemes.
Efficient ion-slicing of InP thin film for Si-based hetero-integration

Integration of high quality single crystalline InP thin film on Si substrate has potential applications in Si-based photonics and high-speed electronics. In this work, the exfoliation of a 634 nm crystalline InP layer from the bulk substrate was achieved by sequential implantation of He ions and H ions at room temperature. It was found that the sequence of He and H ion implantations has a decisive influence on the InP surface blistering and exfoliation, which only occur in the InP pre-implanted with He ions. The exfoliation efficiency first increases and then decreases as a function of H ion implantation fluence. A kinetics analysis of the thermally activated blistering process suggests that the sequential implantation of He and H ions can reduce the InP thin film splitting thermal budget dramatically. Finally, a high quality 2 inch InP-on-Si(100) hetero-integration wafer was fabricated by He and H ion sequential implantation at room temperature in combination with direct wafer bonding.
Ketamine Does Not Exert Protective Properties on Dopaminergic Neurons in the Lactacystin Mouse Model of Parkinson’s Disease

Parkinson’s disease (PD) is an age-related neurodegenerative condition characterized by a progressive loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). A loss of proteasome function participates to the pathogenesis of PD, leading to the development of rodent models in which a proteasome inhibitor is applied to the nigrostriatal pathway. We recently characterized the intranigral lactacystin (LAC) mouse model, leading to nigrostriatal degeneration, motor dysfunction and alpha-synuclein accumulation. In the present study, we compared the effect of two commonly used anesthetics for generating animal models of PD—i.e., ketamine (KET) and isoflurane (ISO)—on the vulnerability of mouse dopaminergic neurons to proteasome inhibition-induced degeneration. Both anesthetics have the potential to affect the susceptibility of the nigrostriatal pathway for toxin-induced degeneration, and are known to modulate dopamine (DA) homeostasis. Yet, their impact on nigrostriatal degeneration in the proteasome inhibition model has not been evaluated. Unilateral injection with LAC in the SNpc of mice induced motor impairment and significantly reduced the number of dopaminergic cells to ~55%, irrespective of the anesthetic used. However, LAC-induced striatal DA depletion was slightly affected by the choice of anesthetic, resulting in a significant increase in DA turnover in the ISO- but not in KET-treated mice. These results suggest that the extent of nigrostriatal dopaminergic neural loss caused by LAC is not influenced by the choice of anesthetic, and that compared to other PD models, KET is not neuroprotective in the LAC model.
Ambient particulate matter enhances the pulmonary allergic immune response to house dust mite in a BALB/c mouse model by augmenting Th2‐ and Th17‐immune responses

Ambient particulate matter (PM) exacerbates airway inflammation and hyper‐reactivity in asthmatic patients. Studies show that PM has adjuvant‐like properties that enhance the allergic inflammatory response; however, the mechanisms through which PM enhances these processes remain elusive. The objective of the study was to examine how ambient PM enhances the allergic immune response. Eight‐week‐old BALB/c mice were sensitized with house dust mite (HDM) or HDM and ambient particulate matter (PM, 2.5 μm; Sacramento, CA) to assess how PM modulates the development of adaptive immune responses against allergens. Both groups were challenged with HDM only. Bronchoalveolar lavage (BAL) was analyzed for extent of airway inflammation. Lung tissue was used for histological analysis, mucosubstance quantification, and heme oxygenase‐1 (HO‐1) localization/quantification. Gene expression was analyzed in whole lung to characterize immune markers of inflammation: cytokines, chemokines, antioxidant enzymes, and transcription factors. Cytokine and chemokine protein levels were quantified in whole lung to confirm gene expression patterns. Compared to HDM‐only sensitization, exposure to PM during HDM sensitization led to significant immune cell recruitment into the airway subepithelium, IgE gene expression, mucosubstance production, and Th2‐associated cytokine expression. HO‐1 levels were not significantly different between the treatment groups. Gene expression profiles suggest that polycyclic aromatic hydrocarbon (PAH) content in PM activated the aryl hydrocarbon receptor (AhR) and enhanced Th17‐responses in the mice that received HDM and PM compared to mice that received HDM‐only. The findings suggest that PM enhances allergic sensitization via enhancement of Th2‐mediated inflammation and that AhR activation by PAHs in PM promotes Th17‐immune responses.
Association of the genetic polymorphisms in immunoinflammatory microRNAs with risk of ischemic stroke and subtypes in an Iranian population

Stroke is one of the most common type of cerebrovascular disease threatening human health and life with high mortality, disability, and morbidity. Ischemic stroke (IS) is determined to be a complex disease containing a group of heterogeneous disorders with various environmental and genetic risk factors. This study evaluated the polymorphisms of microRNAs involved in inflammatory routes leading to stroke in an Iranian population. This study evaluated the associations of hsa‐mir‐608 C/G rs4919510, hsa‐mir‐499 A/G rs3746444, and hsa‐mir‐145 C/T rs190323149 polymorphisms in precursor miRNAs with the risk of IS. These microRNA polymorphisms were analyzed in 470 patients with IS and 489 control subjects. The TOAST criteria was applied for IS subtypes classification. The frequency of the allele G of hsa‐mir‐499/rs3746444 A/G revealed significant association with IS in comparison with controls ( p < 0.0001, OR = 1.838, 95% CI = 1.406–2.401). Increased IS risks were associated with hsa‐mir‐499/ rs3746444 A/G genotypes in diverse genetic model (homozygote comparison: p = 0.004, OR = 2.136, 95% CI = 1.269–3.597; heterozygote comparison: p = 0.029, OR = 1.373, 95% CI = 1.033–1.825). Statistical analysis in IS subtypes showed that cardio‐embolic patients compared with other subtypes (large artery atherosclerosis and lacunar) had higher frequency of G allele (LAA vs. CEI, p = 0.017; LAC vs. CEI, p = 0.009), AG genotype (LAA vs. CEI, p = 0.016; LAC vs. CEI, p = 0.013). Nevertheless, this study did not find any association between the alleles and genotypes of mir‐608 C/G rs4919510 SNP and IS, respectively ( p > 0.05). The current investigation provided verification that hsa‐mir‐499 rs3746444 A/G polymorphism may be associated with a significantly increased risk of IS in an Iranian population.
FasL Modulates Expression of Mmp2 in Osteoblasts

FasL is a well-known actor in the apoptotic pathways but recent reports have pointed to its important novel roles beyond cell death, as observed also for bone cells. This is supported by non-apoptotic appearance of FasL during osteogenesis and by significant bone alterations unrelated to apoptosis in FasL deficient (gld) mice. The molecular mechanism behind this novel role has not yet been revealed. In this report, intramembranous bone, where osteoblasts differentiate directly from mesenchymal precursors without intermediary chondrogenic step, was investigated. Mouse mandibular bone surrounding the first lower molar was used as a model. The stage where a complex set of bone cells (osteoblasts, osteocytes, osteoclasts) is first present during development was selected for an initial examination. Immunohistochemical staining detected FasL in non-apoptotic cells at this stage. Further, FasL deficient vs. wild type samples subjected to osteogenic PCR Array analysis displayed a significantly decreased expression of Mmp2 in gld bone. To examine the possibility of this novel FasL–Mmp2 relationship, intramembranous bone-derived osteoblastic cells (MC3T3-E1) were treated with anti-FasL antibody or rmFasL. Indeed, the FasL neutralization caused a decreased expression of Mmp2 and rmFasL added to the cells resulted in the opposite effect. Since Mmp2-/- mice display age-dependent alterations in the intramembranous bone, early stages of gld mandibular bone were examined and age-dependent phenotype was confirmed also in gld mice. Taken together, the present in vivo and in vitro findings point to a new non-apoptotic function of FasL in bone development associated with Mmp2 expression.
Frequency of cytomegalovirus in fertile and infertile men, referring to Afzalipour Hospital IVF Research Center, Kerman, IRAN: A case-control study

Background: Cytomegalovirus (CMV) virus can hide in urinary genital tract cells and affect male infertility disorders. Objective: To evaluate frequency of CMV in the semen samples of men with infertility problems referring to a in vitro fertilization (IVF) center in Kerman, Iran and its association with the parameters of semen. Materials and Methods: In this case-control study, Real time polymerase chain reaction test was performed for detection of human cytomegalovirus in 100 fertile men compared to 100 infertile men referred to the IVF center of Afzalipour Hospital, Kerman, Iran. Results: Out of 200 samples, 30 samples (15%) were positive for CMV DNA virus (23/100 men (23%) in case group and 7/100 men (7%) in the control group). Sperm counts and motility in the control group were more than the case group (p˂0.0001). There was a significant relationship between the prevalence of CMV infection and male infertility (p˂0.001). Conclusion: Our finding showed that, prevalence of CMV infection was higher in infertile men compared to fertile men and CMV infection can be considered as an important part of male infertility. So; antiviral treatment of positive cases can be effective in improving sperm quality and successful IVF. The relationship between CMV infection in semen and infertility was obtained in previous studies and was confirmed by our study.
High‐density electromyography activity in various hamstring exercises

Proximal‐distal differences in muscle activity are rarely considered when defining the activity level of hamstring muscles. The aim of this study was to determine the inter‐muscular and proximal‐distal electromyography (EMG) activity patterns of hamstring muscles during common hamstring exercises. Nineteen amateur athletes without a history of hamstring injury performed 9 exercises, while EMG activity was recorded along the biceps femoris long head (BFlh) and semitendinosus (ST) muscles using 15‐channel high‐density electromyography (HD‐EMG) electrodes. EMG activity levels normalized to those of a maximal voluntary isometric contraction (%MVIC) were determined for the eccentric and concentric phase of each exercise and compared between different muscles and regions (proximal, middle, distal) within each muscle. Straight‐knee bridge, upright hip extension, and leg curls exhibited the highest hamstrings activity in both the eccentric (40%‐54%MVIC) and concentric phases (69%‐85%MVIC). Hip extension was the only BF‐dominant exercise (Cohen's d = 0.28 (eccentric) and 0.33 (concentric)). Within ST, lower distal than middle/proximal activity was found in the bent‐knee bridge and leg curl exercises (d range = 0.53‐1.20), which was not evident in other exercises. BFlh also displayed large regional differences across exercises (d range = 0.00‐1.28). This study demonstrates that inter‐muscular and proximal‐distal activity patterns are exercise‐dependent, and in some exercises are affected by the contraction mode. Knowledge of activity levels and relative activity of hamstring muscles in different exercises may assist exercise selection in hamstring injury management.
The sex gap in neonatal mortality and the AIDS epidemic in sub-Saharan Africa

The sex gap in early-age death is one of the most important sources of child inequality in all societies, and it carries negative social consequences in the long run. In the absence of gender discrimination in the allocation of foods and heath resources, mortality rates are higher in boys than in girls.1–3 Recent studies however suggest that in sub-Saharan Africa, the general improvement in state capacity and the quality of political and democratic institutions has had stronger health benefits for boys, reducing the male-female gap in early-age mortality.4 5 Democratic indicators such as political participation, competitiveness in the recruitment of the executive and constraints on executive power substantially improved after 1990. These positive developments led to an improvement in the quality of public health institutions. Mabeu and Pongou’s research implies that the health benefits of these positive institutional changes have mostly accrued to boys, in part because these changes have helped constrain the negative influences of the male biological make-up on mortality.5 But this pattern was likely to be specific to HIV-unexposed children. Among HIV-exposed children, it seems that other forces were at play. In this editorial, we analyse trends in the sex gap in neonatal death—death occurring within 1 month of birth-during the era of the AIDS epidemic, and argue that they were sensitive to the availability of antiretroviral medicines. Child exposure to HIV (during pregnancy, delivery and breast feeding) reduced the female survival advantage, but this situation was gradually reversed by the availability of antiretroviral treatment. Our argument is partly captured in figure 1, which shows unadjusted trends in the probability of neonatal death over the period 1960–2017 for both boys and girls in sub-Saharan Africa. Neonatal mortality declined substantially over this period for both sexes. However, as figure 2 shows, the decline was …
Acromioclavicular joint injuries: diagnosis, classification and ligamentoplasty procedures

Acromioclavicular (AC) joint injury is a frequent diagnosis after an acute shoulder trauma – often found among athletes and people involved in contact sports. This injury occurs ﬁve times more frequently in men than in women, with the highest incidence in the 20- to 30-year-old age group. Patients usually complain of pain and tenderness over the shoulder, particularly over the AC joint. Depending on the degree of injury, the clavicle may become prominent on the injured site. The original classification was described by Rockwood and Green according to the injured ligament complex and degree and direction of clavicular displacement. Many surgical procedures have been described; among these are screws, plates, muscle transfer, ligamentoplasty procedures and ligament reconstruction using either autograft or allografts. With the advancement of shoulder arthroscopy, surgeons are much more capable of performing mini-open or arthroscopically-assisted procedures, allowing patients an earlier return to their daily living activities. However, the results of conventional open techniques are still comparable. The introduction of new arthroscopic equipment provides a great variety of surgical procedures, though every new technique has its own advantages and pitfalls. Currently there is no gold standard for the surgical treatment of any type of AC injury, though it should be remembered that whenever an arthroscopic technique is chosen, the surgeon’s expertise is likely to be the most significant factor affecting outcome. Cite this article: EFORT Open Rev 2018;3:426-433. DOI: 10.1302/2058-5241.3. 170027
Glycosylation in the Thyroid Gland: Vital Aspects of Glycoprotein Function in Thyrocyte Physiology and Thyroid Disorders

The key proteins responsible for hormone synthesis in the thyroid are glycosylated. Oligosaccharides strongly affect the function of glycosylated proteins. Both thyroid-stimulating hormone (TSH) secreted by the pituitary gland and TSH receptors on the surface of thyrocytes contain N-glycans, which are crucial to their proper activity. Thyroglobulin (Tg), the protein backbone for synthesis of thyroid hormones, is a heavily N-glycosylated protein, containing 20 putative N-glycosylated sites. N-oligosaccharides play a role in Tg transport into the follicular lumen, where thyroid hormones are produced, and into thyrocytes, where hyposialylated Tg is degraded. N-glycans of the cell membrane transporters sodium/iodide symporter and pendrin are necessary for iodide transport. Some changes in glycosylation result in abnormal activity of the thyroid and alteration of the metabolic clearance rate of hormones. Alteration of glycan structures is a pathological process related to the progression of chronic diseases such as thyroid cancers and autoimmunity. Thyroid carcinogenesis is accompanied by changes in sialylation and fucosylation, β1,6-branching of glycans, the content and structure of poly-LacNAc chains, as well as O-GlcNAcylation, while in thyroid autoimmunity the main processes affected are sialylation and fucosylation. The glycobiology of the thyroid gland is an intensively studied field of research, providing new data helpful in understanding the role of the sugar component in thyroid protein biology and disorders.
The adaptive significance of chromosomal inversion polymorphisms in Drosophila melanogaster

Chromosomal inversions, structural mutations that reverse a segment of a chromosome, cause suppression of recombination in the heterozygous state. Several studies have shown that inversion polymorphisms can form clines or fluctuate predictably in frequency over seasonal time spans. These observations prompted the hypothesis that chromosomal rearrangements might be subject to spatially and/or temporally varying selection. Here, we review what has been learned about the adaptive significance of inversion polymorphisms in the vinegar fly Drosophila melanogaster, the species in which they were first discovered by Sturtevant in 1917. A large body of work provides compelling evidence that several inversions in this system are adaptive; however, the precise selective mechanisms that maintain them polymorphic in natural populations remain poorly understood. Recent advances in population genomics, modelling and functional genetics promise to greatly improve our understanding of this long‐standing and fundamental problem in the near future.
Dispersal Modifies the Diversity and Composition of Active Bacterial Communities in Response to a Salinity Disturbance

Dispersal can influence the response of bacterial communities to environmental changes and disturbances. However, the extent to which dispersal contributes to the community response in dependence of the character and strength of the disturbance remains unclear. Here, we conducted a transplant experiment using dialysis bags in which bacterioplankton originating from brackish and marine regions of the Saint Lawrence Estuary were reciprocally incubated in the two environments for 5 days. Dispersal treatments were set-up by subjecting half of the microcosms in each environment to an exchange of cells between the marine and brackish assemblages at a daily exchange rate of 6% (v/v), and the other half of microcosms were kept as the non-dispersal treatments. Bacterial 16S rRNA sequencing was then used to examine the diversity and composition of the active communities. Alpha diversity of the marine communities that were exposed to the brackish environment was elevated greatly by dispersal, but declined in the absence of dispersal. This indicates that dispersal compensated the loss of diversity in the marine communities after a disturbance by introducing bacterial taxa that were able to thrive and coexist with the remaining community members under brackish conditions. On the contrary, alpha diversity of the brackish communities was not affected by dispersal in either environment. Furthermore, dispersal led to an increase in similarity between marine and brackish communities in both of the environments, with a greater similarity when the communities were incubated in the brackish environment. These results suggest that the higher initial diversity in the brackish than in the marine starting community made the resident community less susceptible to dispersing bacteria. Altogether, this study shows that dispersal modifies the diversity and composition of the active communities in response to a salinity disturbance, and enables the local adjustment of specific bacteria under brackish environmental conditions.
Switching Isotropic and Directional Exploration with Parameter Space Noise in Deep Reinforcement Learning

This paper proposes an exploration method for deep reinforcement learning based on parameter space noise. Recent studies have experimentally shown that parameter space noise results in better exploration than the commonly used action space noise. Previous methods devised a way to update the diagonal covariance matrix of a noise distribution and did not consider the direction of the noise vector and its correlation. In addition, fast updates of the noise distribution are required to facilitate policy learning. We propose a method that deforms the noise distribution according to the accumulated returns and the noises that have led to the returns. Moreover, this method switches isotropic exploration and directional exploration in parameter space with regard to obtained rewards. We validate our exploration strategy in the OpenAI Gym continuous environments and modified environments with sparse rewards. The proposed method achieves results that are competitive with a previous method at baseline tasks. Moreover, our approach exhibits better performance in sparse reward environments by exploration with the switching strategy.