Miracle-dz/UniFAR-FTUs huggingface dataset:
A Simulator and Benchmark for the RingWorld Protocol

RingWorld is a new consensus protocol aiming for deployment in datacenters that utilizes programmable top-of-rack (ToR) switches and multiple servers in a rack. The ToRs connect to each other and form a logical ring. This report attempts to build a simulator for RingWorld protocol’s normal execution model, and to benchmark the protocol.
Hepatitis A and E Viruses in Mussels from Cherrat Estuary in Morocco: Detection by Real-Time Reverse Transcription PCR Analysis

The aim of the present study was to evaluate hepatitis A virus (HAV) and hepatitis E virus (HEV) contamination in mussels (Mytilus galloprovincialis) from Cherrat estuary (Moroccan Atlantic Coast), Morocco. In total, 52 samples (n = 12 mussels/each) were collected at four sites in the estuary, monthly, between March 2019 and March 2020. HAV and HEV were detected by real-time reverse transcription polymerase chain reaction (RT-PCR) according to the ISO/TS 15216 method. HAV was detected in 46.15% of analyzed samples. Conversely, HEV was not detected in any sample. Moreover, the HAV detection rate was significantly associated with seasonal rainfall variations. This qualitative study on HAV and HEV contamination highlights the interest of studying mussel samples from wild areas. As HAV presence in mussels represents a potential health risk, viral contamination surveillance of mussels is necessary to protect consumers. HAV shellfish contamination must be monitored at Cherrat estuary because of the role played by shellfish as HAV reservoirs and/or vehicles in fecal-oral HAV transmission.
An Integrated Analytical Approach for the Characterization of Probiotic Strains in Food Supplements

Research surrounding health benefits from probiotics is becoming popular because of the increasing demand for safer products with protective and therapeutic effects. Proven benefits are species- or genus-specific; however, no certified assays are available for their characterization and quantification at the strain level in the food supplement industry. The objective of this study was to develop a strain-specific Real-time quantitative polymerase chain reaction (RT-qPCR)-based method to be implemented in routine tests for the identification and quantification of Bifidobacterium longum, Bifidobacterium animalis spp. lactis, Lactobacillus paracasei, Lactobacillus rhamnosus, Lactobacillus casei, Bifidobacterium breve, Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus helveticus, starting from a powder mixture of food supplements. The method optimization was carried out in combination with flow cytometry to compare results between the two strategies and implement the analytical workflow with the information also regarding cell viability. These assays were validated in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) criteria using the plate count enumeration as the gold standard reference. Briefly, probiotic DNAs were extracted from two powder food supplements. Strain-specific primers targeting unique sequence regions of 16S RNA were identified and amplified by RT-qPCR. Primers were tested for specificity, sensitivity, and efficiency. Both RT-qPCR and flow-cytometry methods described in our work for the quantification and identification of Lactobacillus and Bifidobacterium strains were specific, sensitive, and precise, showing better performances with respect to the morphological colony identification. This work demonstrated that RT-qPCR can be implemented in the quality control workflow of commercial probiotic products giving more standardized and effective results regarding species discrimination.
Snapshot into the Type-2-Diabetes-Associated Microbiome of a Romanian Cohort

The prevalence of type 2 diabetes mellitus (T2D) is alarmingly increasing worldwide, urgently calling for a better understanding of the underlying mechanisms in order to step up prevention and improve therapeutic approaches. It is becoming evident that the gut microbiota seem to have an endless capacity to impact T2D. In this study, we profile the gut microbiome patterns in T2D patients from Romania, by using quantitative Real-Time PCR and next generation sequencing. We enrolled a total of 150 individuals (105 T2D patients, 50 of them without metformin treatment and 45 healthy volunteers). The levels of potentially beneficial butyrate-producing bacteria were significantly reduced, while potentially pathogenic microorganisms such as Enterobacteriaceae and Fusobacterium were enriched in T2D patients. We evaluated the correlation between clinical parameters and gut microbiota and identified the genera Bacteroides, Alistipes, Dialister, Bilophila and Sutterella as possible detrimental factors in T2D. Our findings suggest that the gut microbiota may be a potential target in novel approaches to halt the development of T2D-associated complications.
Metagenome-Based Exploration of Bacterial Communities Associated with Cyanobacteria Strains Isolated from Thermal Muds

Cyanobacteria constitute a pioneer colonizer of specific environments for whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through the exchange and recycling of key nutrients and the sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated, along with their associated cyanospheres, from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among the members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic descriptions of the microbial consortia. The results provided insights into the potential role and metabolic capabilities of the microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity, and genetic potential functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlighted the great influence of the reference protein database chosen for performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately covers both autotroph and heterotroph metabolic specificities.
A Data Collection Protocol, Tool and Analysis for the Mapping of Speech Volume to Avatar Facial Animation

Knowing the relationship between speech-related facial movement and speech is important for avatar animation. Accurate facial displays are necessary to convey perceptual speech characteristics fully. Recently, an effort has been made to infer the relationship between facial movement and speech with data-driven methodologies using computer vision. To this aim, we pro-pose to use blendshape-based facial movement tracking, because it can be easily translated to avatar movement. Furthermore, we present a protocol for audio-visual and behavioral data collection and a tool running on WEB that aids in collecting and synchronizing data. As a start, we provide a database of six Japanese participants reading emotion-related scripts at different volume levels. Using this methodology, we found a relationship between speech volume and facial movement around the nose, cheek, mouth, and head pitch. We hope that our protocols, WEB-based tool, and collected data will be useful for other scientists to derive models for avatar animation.
The harmonic map problem with mixed boundary conditions

Given two polygons S ⊂ R 2 and Σ ⊂ R m with the same number of sides, we prove the existence and uniqueness of a smooth harmonic map u : S → R m satisfying the mixed boundary conditions for S and Σ. This solution is constructed and characterized as a minimizer of the Dirichlet’s energy in the class of maps which satisfy the ﬁrst mixed boundary condition. Several properties of the solution are established. We also discuss the mixed boundary conditions for harmonic maps deﬁned in smooth domains of the plane.
Single-cell RNA sequencing reveals the Müller subtypes and inner blood–retinal barrier regulatory network in early diabetic retinopathy

As the basic pathological changes of diabetic retinopathy (DR), the destruction of the blood-retina barrier (BRB) and vascular leakage have attracted extensive attention. Without timely intervention, BRB damage will eventually lead to serious visual impairment. However, due to the delicate structure and complex function of the BRB, the mechanism underlying damage to the BRB in DR has not been fully clarified. Here, we used single-cell RNA sequencing (RNA-seq) technology to analyze 35,910 cells from the retina of healthy and streptozotocin (STZ)-induced diabetic rats, focusing on the degeneration of the main cells constituting the rat BRB in DR and the new definition of two subpopulations of Müller cells at the cell level, Ctxn3+Müller and Ctxn3−Müller cells. We analyzed the characteristics and significant differences between the two groups of Müller cells and emphasized the importance of the Ctxn3+Müller subgroup in diseases. In endothelial cells, we found possible mechanisms of self-protection and adhesion and recruitment to pericytes. In addition, we constructed a communication network between endothelial cells, pericytes, and Müller subsets and clarified the complex regulatory relationship between cells. In summary, we constructed an atlas of the iBRB in the early stage of DR and elucidate the degeneration of its constituent cells and Müller cells and the regulatory relationship between them, providing a series of potential targets for the early treatment of DR.
A theoretical study of the critical radius of precipitates and its application to silicon oxide in silicon

A theoretical expression is derived describing the influence of the extrinsic and intrinsic point‐defect concentration and of the strain energy on the critical radius of precipitates. It is shown that an exponential distribution of the precipitate radii leads to analytical expressions for the content of precipitating species present under the form of sub‐ and supercritical precipitate nuclei. The application of the obtained theoretical results is illustrated by a few case studies on silicon‐oxide precipitates in silicon. Excellent agreement between the calculated and observed subcritical oxygen content in as‐grown Czochralski silicon is obtained.
Survivors and colonizers: Contrasting biogeographic histories reconciled in the Antarctic freshwater copepod Boeckella poppei

Two main hypotheses have been proposed to explain the contemporary distribution of Antarctic terrestrial biota. We assess whether the current distribution of maritime Antarctic populations of the freshwater copepod Boeckella poppei is the result of (1) a post-Last Glacial Maximum (LGM) colonization, or whether (2) the species survived in regional glacial refugia throughout the LGM and earlier glaciations. Using 438 specimens from 34 different sampling sites across Southern South America, South Georgia, South Orkney Islands, South Shetland Islands, and the Antarctic Peninsula, we analyzed mitochondrial and nuclear sequences to uncover patterns of genetic diversity and population structure. We also performed median-joining haplotype network, phylogenetic reconstruction, and divergence time analyses. Finally, we evaluated past demographic changes and historical scenarios using the Approximate Bayesian Computation (ABC) method. Our data support the existence of two clades with different and contrasting biogeographic histories. The first clade has been present in maritime Antarctica since at least the mid-Pleistocene, with the South Orkney Islands the most likely refugial area. The second clade has a broader distribution including southern South America, South Georgia, South Shetland Islands, and the Antarctic Peninsula. The ABC method identified long-distance dispersal (LDD) colonization event(s) from southern South America to South Georgia and the maritime Antarctic after the LGM deglaciation, supporting more recent colonization of Antarctic locations. The current Antarctic and sub-Antarctic distribution of B. poppei is likely derived from two independent biogeographic events. The combination of both (1) post-LGM colonization from southern South America and (2) longer-term persistence in in situ regional refugia throughout glacial periods challenges current understanding of the biogeographic history of Antarctic freshwater biota. Re-colonization of ice-impacted Antarctic areas would have occurred following a LDD and Establishment model, pointing to the existence of possible post-dispersal barriers, despite widely assumed high passive dispersal capacity in freshwater invertebrates.
Is transcranial direct current stimulation beneficial for treating pain, depression, and anxiety symptoms in patients with chronic pain? A systematic review and meta-analysis

Background Chronic pain is often accompanied by emotional dysfunction. Transcranial direct current stimulation (tDCS) has been used for reducing pain, depressive and anxiety symptoms in chronic pain patients, but its therapeutic effect remains unknown. Objectives To ascertain the treatment effect of tDCS on pain, depression, and anxiety symptoms of patients suffering from chronic pain, and potential factors that modulate the effectiveness of tDCS. Methods Literature search was performed on PubMed, Embase, Web of Science, and Cochrane Library from inception to July 2022. Randomized controlled trials that reported the effects of tDCS on pain and depression and anxiety symptoms in patients with chronic pain were included. Results Twenty-two studies were included in this review. Overall pooled results indicated that the use of tDCS can effectively alleviate short-term pain intensity [standard mean difference (SMD): −0.43, 95% confidence interval (CI): −0.75 to −0.12, P = 0.007] and depressive symptoms (SMD: −0.31, 95% CI, −0.47 to −0.14, P < 0.001), middle-term depressive symptoms (SMD: −0.35, 95% CI: −0.58 to −0.11, P = 0.004), long-term depressive symptoms (ES: −0.38, 95% CI: −0.64 to −0.13, P = 0.003) and anxiety symptoms (SMD: −0.26, 95% CI: −0.51 to −0.02, P = 0.03) compared with the control group. Conclusion tDCS may be an effective short-term treatment for the improvement of pain intensity and concomitant depression and anxiety symptoms in chronic pain patients. Stimulation site, stimulation frequency, and type of chronic pain were significant influence factors for the therapeutic effect of tDCS. Systematic review registration https://www.crd. york.ac. uk/PROSPERO/display_record. php? RecordID=297693, identifier: CRD42022297693.
Microwave remote sensing for agricultural drought monitoring: Recent developments and challenges

Agricultural droughts are extreme events which are often a result of interplays between multiple hydro-meteorological processes. Therefore, assessing drought occurrence, extent, duration and intensity is complex and requires the combined use of multiple variables, such as temperature, rainfall, soil moisture (SM) and vegetation state. The benefit of using information on SM and vegetation state is that they integrate information on precipitation, temperature and evapotranspiration, making them direct indicators of plant available water and vegetation productivity. Microwave remote sensing enables the retrieval of both SM and vegetation information, and satellite-based SM and vegetation products are available operationally and free of charge on a regional or global scale and daily basis. As a result, microwave remote sensing products play an increasingly important role in drought monitoring applications. Here, we provide an overview of recent developments in using microwave remote sensing for large-scale agricultural drought monitoring. We focus on the intricacy of monitoring the complex process of drought development using multiple variables. First, we give a brief introduction on fundamental concepts of microwave remote sensing together with an overview of recent research, development and applications of drought indicators derived from microwave-based satellite SM and vegetation observations. This is followed by a more detailed overview of the current research gaps and challenges in combining microwave-based SM and vegetation measurements with hydro-meteorological data sets. The potential of using microwave remote sensing for drought monitoring is demonstrated through a case study over Senegal using multiple satellite- and model-based data sets on rainfall, SM, vegetation and combinations thereof. The case study demonstrates the added-value of microwave-based SM and vegetation observations for drought monitoring applications. Finally, we provide an outlook on potential developments and opportunities.
β-lactam precision dosing in critically ill children: Current state and knowledge gaps

There has been emerging interest in implementing therapeutic drug monitoring and model-informed precision dosing of β-lactam antibiotics in critically ill patients, including children. Despite a position paper endorsed by multiple international societies that support these efforts in critically ill adults, implementation of β-lactam precision dosing has not been widely adopted. In this review, we highlight what is known about β-lactam antibiotic pharmacokinetics and pharmacodynamics in critically ill children. We also define the knowledge gaps that present barriers to acceptance and implementation of precision dosing of β-lactam antibiotics in critically ill children: a lack of consensus on which subpopulations would benefit most from precision dosing and the uncertainty of how precision dosing changes outcomes. We conclude with opportunities for further research to close these knowledge gaps.
Antibiotic use, knowledge, and practices of milk vendors in India's informal dairy value chain

Background Milk vendors play an important role in India's dairy value chain; however, their food safety practices are poorly understood. From a milk safety perspective, vendor behavior is significant because it has the potential to affect both consumer and producer behavior. This study describes the types of milk vendors in two Indian states, in an attempt to investigate vendors' hygienic knowledge and practices toward safety and antimicrobial resistance (AMR). Methods A cross-sectional study was conducted in the states of Assam and Haryana, India. In selected villages, all the milk vendors identified at the time of visit were interviewed. A questionnaire was used to assess the knowledge and practices on antibiotics, milk safety and hygiene. The milk samples were tested for presence of antibiotic resistant bacteria using antibiotic susceptibility testing. Results In total, 244 milk vendors were interviewed during the survey. Out of these, 146 (59.8%) of the vendors traded raw milk, while 40.2% traded pasteurized milk. Vendors were categorized depending on whom they supplied milk to. Five categories were identified: (a) those who sold at grocery shops; (b) those who sold on roadside (roadside vendors); (c) those who sold from door to door; (d) those who sold to sweet makers/tea stalls, and (e) those who sold from own home/other entity. The level of training among vendors on milk hygiene was non-existent and the knowledge related to antibiotics was low. Most of them [210/244 (86.07%)] agreed that boiled milk is always safer than raw milk but almost half [119 (48.77%)] of them admitted that sometimes they drink milk without boiling it. Most vendors believed that they could identify whether milk is safe or not for consumption just by its appearance and smell. Out of 124 milk samples collected from surveyed milk vendors and tested for the presence of antibiotic-resistant bacteria, 80 (64.52%) were tested positive. Conclusion This study highlights the low levels of knowledge regarding food safety among milk vendors. It shows the predominance of informal milk vendors in the surveyed states and prevalence of AMR bacteria in milk traded by them. Training may be a beneficial strategy for addressing the issue.
Association of prescribed oral stimulants on cocaine use among patients enrolled in opioid agonist treatment: A retrospective longitudinal cohort study

Objectives The objective of this study was to measure the association of prescribed oral stimulants with the consumption of cocaine among a population of patients receiving Opioid Agonist Therapy (OAT). Methods The study was a retrospective clinical cohort study using the medical records of all patients receiving OAT who attended treatment clinics within the Canadian Addiction Treatment Centers (CATC) in Ontario from April 2014 to February 2021. Linear mixed-effects models were fit for the exposure of prescribed oral stimulants, and the outcome of a positive urinalysis drug screen for cocaine. Covariates for age, sex, and a random effect for patients were fitted to account for differences between and within patient observations over time. Results Among patients receiving OAT therapy n = 314 patients were prescribed oral stimulants and n = 11,879 patients were not prescribed oral stimulants among Ontario CATC clinics (n = 92, n = 145 physicians), the mean age at enrollment for patients receiving oral stimulants was 37.0, SD = 8.8, with 43.6% female patients and for patients not receiving oral stimulants mean age was 36.6, SD = 10.7, with 39.6% female patients. Linear mixed effects models showed no difference in cocaine-positive urine tests over time for fixed effects B = 0.001, however, when considering the Interclass correlation coefficient (ICC) between the fixed effects, we found that time since the prescription of an oral stimulant was associated with a decrease of ICC = −0.14 in cocaine positive urine tests. Increasing age at prescription ICC = −0.92, and being male ICC = −0.23 were associated with decreasing cocaine-positive urine. Conclusion The use of oral stimulant prescriptions to treat cocaine use had no clinically significant benefit in a real-world setting. Patients who receive prescriptions for oral stimulants consume more cocaine before and after treatment compared to patients without an oral stimulant prescription. We also observed that cocaine use was reduced with increased time since treatment initiation.