Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Pathogenic Bacteria Among Adult Ticks Collected in Conservation Areas and Private Lands of Adair County, Missouri

Abstract: Three species of ticks have been found in Northeast Missouri, where the incidence and prevalence of tick-borne infections is among the highest in the United States of America. We collected ticks and detected the presence of Rickettsia montanensis (instead of R. rickettsii) and Ehrlichia chaffeensis and the absence of Anaplasma phagocytophilum infections among adult ticks collected in conservation and private areas of Adair County, Missouri. Pathogens were detected and identified using PCR, DNA sequencing of PCR fragments and statistical sequence analysis. We found Ehrlichia chaffeensis in 10% of ticks of the species Amblyomma amercanum and Rickettsia montanensis in 7.95% of collected ticks of the species Dermacentor variabilis. These findings stress the importance of continuous monitoring and study of vector populations in the region. Such monitoring can contribute to risk assessment of ehrlichiosis, spotted fever infections, and anaplasmosis, which are considered endemic in the region.
The Great Internet TCP Congestion Control Census

In 2016, Google proposed and deployed a new TCP variant called BBR. BBR represents a major departure from traditional congestion control as it uses estimates of bandwidth and round-trip delays to regulate its sending rate. BBR has since been introduced in the upstream Linux kernel and deployed by Google across its data centers. Since the last major study to identify TCP congestion control variants on the Internet was done before BBR, it is timely to conduct a new census to give us a sense of the current distribution of congestion control variants on the Internet. To this end, we designed and implemented Gordon, a tool that allows us to measure the congestion window (cwnd) corresponding to each successive RTT in the TCP connection response of a congestion control algorithm. To compare a measured flow to the known variants, we created a localized bottleneck and introduced a variety of network changes like loss events, changes in bandwidth and delay, while normalizing all measurements by RTT. We built an offline classifier to identify the TCP variant based on the cwnd trace over time. Our results suggest that CUBIC is currently the dominant TCP variant on the Internet, and is deployed on about 36% of the websites in the Alexa Top 20,000 list. While BBR and its variant BBR G1.1 are currently in second place with a 22% share by website count, their present share of total Internet traffic volume is estimated to be larger than 40%. We also found that Akamai has deployed a unique loss-agnostic rate-based TCP variant on some 6% of the Alexa Top 20,000 websites and there are likely other undocumented variants. Therefore, the traditional assumption that TCP variants ''in the wild'' will come from a small known set is not likely to be true anymore. Our results suggest that some variant of BBR seems poised to replace CUBIC as the next dominant TCP variant on the Internet.
Transmission of SARS-CoV-2, Required Developments in Research and Associated Public Health Concerns

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is rapidly spreading across the world to cause thousands of mortalities each day. Poor responses from the authorities to the spread of infection, lack of effective measures for prevention, unavailability of promising treatment options, and sufficient diagnostic options have created an alarming for the world. The transmission routes from human to human of SARS-CoV-2 can be the direct transmission, droplet inhalation transmission, contact transmission, transmission through saliva, and transmission via fecal–oral routes. Due to the asymptomatic spread of SARS-CoV-2's, developing control and prevention measures is challenging. Implementing proper strategies addressing the infection control and clinical supplies, understanding the mechanism associated with pathogenesis, advancing in preventive measures and effective treatment and diagnostic options are necessary to control the ongoing pandemic. In this article, we briefly discuss the features, entry mechanism, infectiousness, and health consequences related to the COVID-19 outbreak.
Using Systolic Local Mechanical Load to Predict Fiber Orientation in Ventricles

A simple rule adopted for myofiber reorientation in the ventricles is pursued by taking the microscopic branching network of myocytes into account. The macroscopic active tension generated on the microscopic branching structure is modeled by a multidirectional active stress tensor, which is defined as a function of the strains in the branching directions. In our reorientation algorithm, the principal direction of the branching network is updated so that it turns in the direction of greater active tension in the isovolumetric systole. Updates are performed step-by-step after the mechanical equilibrium has been attained with the current fiber structure. Starting from a nearly flat distribution of the principal fiber orientation along the circumferential direction, the reoriented fiber helix angles range from 70 to 40° at epicardium and from 60 to 80° at endocardium, in agreement with experimental observations. The helical ventricular myocardial band of Torrent-Guasp’s model and the apical spiral structure of Rushmer’s model are also reconstructed by our algorithm. Applying our algorithm to the infarcted ventricle model, the fiber structure near the infarcted site is remodeled so that the helix angle becomes steeper with respect to the circumferential direction near the epicardial surface. Based on our numerical analysis, we draw the following conclusions. (i) The multidirectional active tension based on the microscopic branching network is potentially used to seek tighter connection with neighboring aggregates. (ii) The thickening and thinning transitions in response to active tension in each myocyte allow the macroscopic principal fiber orientation of the microscopic branching network to move toward the direction of greater active tension. (iii) The force–velocity relationship is the key factor in transferring the fiber shortening strain to the magnitude of active tensions used in the myofiber reorientation. (iv) The algorithm naturally leads to homogeneity in the macroscopic active tension and the fiber shortening strain, and results in near-optimal pumping performance. (v) However, the reorientation mechanism may degrade the pumping performance if there is severely inhomogeneous contractility resulting from infarction. Our goal is to provide a tool to predict the fiber architecture of various heart disease patients for numerical simulations of their treatment plans.
Differential Susceptibility and Vulnerability of Brain Cells in C57BL/6 Mouse to Mitochondrial Dysfunction Induced by Short-Term Cuprizone Exposure

Cuprizone (CPZ) is a chemical chelator toxic to mitochondria of cells. While inducing oligodendrocyte (OL) loss and demyelination, CPZ caused no fatal damage to the other brain cells (neurons, astrocytes, and microglia) in previous studies, suggesting differential susceptibility and vulnerability of brain cells to the CPZ intoxication. To demonstrate this interpretation, C57BL/6 mice were fed rodent chow without or with CPZ (0.2%, w/w) for 7 days. One day later, mitochondrial function of brain cells was assessed by proton magnetic resonance spectroscopy (1H-MRS) and biochemical analysis. Another batch of mice were processed to localize the CPZ-induced damage to mitochondrial DNA, label brain cells, and identify apoptotic cells. Compared to controls, CPZ-exposed mice showed significantly lower levels of N-acetyl-L-aspartate, phosphocreatine, and ATP detected by 1H-MRS, indicating mitochondrial dysfunction in brain cells. Susceptibility analysis showed an order of OLs, microglia, and astrocytes from high to low, in terms of the proportion of 8-OHdG labeled cells in each type of these cells in corpus callosum. Vulnerability analysis showed the highest proportion of caspase-3 positive cells in labeled OLs in cerebral cortex and hippocampus, where neurons showed no caspase-3 labeling, but the highest proportion of 8-OHdG labeling, indicating a lowest vulnerability but highest susceptibility to CPZ-induced mitochondrial dysfunction. Immature OLs, microglia, and astrocytes showed adaptive changes in proliferation and activation in response to CPZ-exposure. These data for the first time demonstrated the CPZ-induced mitochondria dysfunction in brain cells of living mouse and specified the differential susceptibility and vulnerability of brain cells to the CPZ intoxication.
African Swine Fever: Lessons to Learn From Past Eradication Experiences. A Systematic Review

Prevention, early detection, prompt reaction, and communication play a crucial role in African swine fever (ASF) control. Appropriate surveillance capable of early detection of the disease in both domestic and wild animals, and the implementation of consolidated contingency plans, are currently considered the best means of controlling this disease. The purpose of this study was to understand the lessons to be learned through the global disease eradication history. To establish which strategies were successful for prevention, control, and eradication of ASF, and which errors should not be repeated, we conducted a systematic review. A query was defined to search for surveillance and control strategies applied by countries worldwide for ASF eradication in the past. Inclusion and exclusion criteria were defined. Decisions on study eligibility and data extraction were performed by two independent reviewers and the differences were resolved by consensus or by a third reviewer. From 1,980 papers, 23 were selected and included in the qualitative analysis. Reports from Belgium, Brazil, Cuba, the Dominican Republic and Haiti, France, mainland Italy, Malta, Portugal, and Spain were included. Despite the economic resources allocated and the efforts made, eradication was possible in only eight countries, between the 50s and 90s in the twentieth century, in different epidemiological and cultural contexts, in some instances within <1 year, and in others in about 40 years. Classical surveillance strategies, such as active and passive surveillance, both at farm and slaughterhouse levels, targeted surveillance, together with conventional biosafety and sanitary measures, led to eradication even in countries in which the tick's epidemiological role was demonstrated. Historical surveillance data analysis indicated that eradication was possible even when technological tools either were not available or were used less than they are currently. This emphasizes that data on surveillance and on animal population are crucial for planning effective surveillance, and targeting proper control and intervention strategies. This paper demonstrates that some strategies applied in the past were effective; these could be implemented and improved to confront the current epidemiological wave. This offers encouragement for the efforts made particularly in Europe during the recent epidemics.
Atmospheric CO2 Concentration and N Availability Affect the Balance of the Two Photosystems in Mature Leaves of Rice Plants Grown at a Free-Air CO2 Enrichment Site

Atmospheric CO2 concentration ([CO2]) has been substantially increasing. Responses of leaf photosynthesis to elevated [CO2] have been intensively investigated because leaf photosynthesis is one of the most important determinants of crop yield. The responses of photosynthesis to elevated [CO2] can depend on nitrogen (N) availability. Here, we aimed to investigate the significance of the appropriate balance between two photosystems [photosystem I (PSI) and photosystem II (PSII)] under various [CO2] and N levels, and thus to clarify if responses of photosynthetic electron transport rates (ETRs) of the two photosystems to elevated [CO2] are altered by N availability. Thus, we examined parameters of the two photosystems in mature leaves of rice plants grown under two [CO2] levels (ambient and 200 μmol mol–1 above ambient) and three N fertilization levels at the Tsukuba free-air CO2 enrichment experimental facility in Japan. Responses of ETR of PSII (ETRII) and ETR of PSI (ETRI) to [CO2] levels differed among N levels. When moderate levels of N were applied (MN), ETRI was higher under elevated [CO2], whereas at high levels of N were applied (HN), both ETRII and ETRI were lower under elevated [CO2] compared with ambient [CO2]. Under HN, the decreases in ETRII and ETRI under elevated [CO2] were due to increases in the non-photochemical quenching of PSII [Y(NPQ)] and the donor side limitation of PSI [Y(ND)], respectively. The relationship between the effective quantum yields of PSI [Y(I)] and PSII [Y(II)] changed under elevated [CO2] and low levels of N (LN). Under both conditions, the ratio of Y(I) to Y(II) was higher than under other conditions. The elevated [CO2] and low N changed the balance of the two photosystems. This change may be important because it can induce the cyclic electron flow around PSI, leading to induction of non-photochemical quenching to avoid photoinhibition.
DNA homology studies of rhizobia from Cicer arietinum L.

The taxonomic status of rhizobia which infect Cicer arietinum is poorly defined. Historically these organisms have been placed under Rhizobium leguminosarum; however, later reports suggested that they be treated as a separate cross-inoculation group. Therefore, DNA homology tests were carried out with various rhizobia. The data indicate that rhizobia from Cicer cannot be placed under any of the recognised species of Rhizobium.
Validation of the Levenson Self-Report Psychopathy Scale in Bulgarian Substance-Dependent Individuals

The co-occurrence of psychopathy and substance use disorders (SUDs) is associated with higher relapse rates and increased risk of violent offending. Studies on the validity of psychopathy measures in community samples and substance-dependent individuals (SDIs) are scarce. The aim of the current study was to examine the psychometric properties of the Levenson Self-Report Psychopathy Scale (LSRP) in a sample of Bulgarian SDIs and non-dependent controls. We tested 615 participants: 106 heroin users, 91 amphetamine users, 123 polysubstance users, and 295 controls. Confirmatory factor analyses replicated the tri-factor structure of the LSRP (egocentric, antisocial, callous). The scale demonstrated acceptable reliability and validity. SDIs scored significantly higher than controls on the total scale and subscales of the LSRP, indicating good discriminant validity. Overall, results indicate that the LSRP is a valid instrument for measuring psychopathy in Bulgarian community samples.
Blind Manipulation of Deformable Objects Based on Force Sensing and Finite Element Modeling

In this paper, we present a novel pipeline to simultaneously estimate and manipulate the deformation of an object using only force sensing and an FEM model. The pipeline is composed of a sensor model, a deformation model and a pose controller. The sensor model computes the contact forces that are used as input to the deformation model which updates the volumetric mesh of a manipulated object. The controller then deforms the object such that a given pose on the mesh reaches a desired pose. The proposed approach is thoroughly evaluated in real experiments using a robot manipulator and a force-torque sensor to show its accuracy in estimating and manipulating deformations without the use of vision sensors.
Localization and local translation of Arc/Arg3.1 mRNA at synapses: some observations and paradoxes

Arc is a unique immediate early gene whose expression is induced as synapses are being modiﬁed during learning.The uniqueness comes from the fact that newly synthesized Arc mRNA is rapidly transported throughout dendrites where it localizes near synapses that were recently activated. Here, we summarize aspects of Arc mRNA translation in dendrites in vivo , focusing especially on features of its expression that are paradoxical or that donot ﬁt in with current models of how Arc protein operates. Findings from in vivo studies that donot quite ﬁt include: (1) Following induction of LTP in vivo , Arc mRNA and protein localize near active synapses, but are also distributed throughout dendrites. In contrast, Arc mRNA localizes selectively near active synapses when stimulation is continued as Arc mRNA is transported into dendrites; (2) Strong induction of Arc expression as a result of a seizure does not lead to a rundown of synaptic efﬁcacy in vivo as would be predicted by the hypothesis that high levels of Arc cause glutamate receptor endocytosis and LTD. (3) Arc protein is synthesized in the perinuclear cytoplasm rapidly after transcriptional activation, indicating that at least a pool of Arc mRNA is not translationally repressed to allow for dendritic delivery; (4) Increases in Arc mRNA in dendrites are not paralleled by increases in levels of exon junction complex (EJC) proteins. These results of studies of mRNA trafﬁcking in neurons in vivo provide a new perspective on the possible roles of Arc in activity-dependent synaptic modiﬁcations. tradition William T. Greenough. it is primarily Arc
Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi

Significance Scrub typhus is a neglected tropical disease caused by the bacterium Orientia tsutsugamushi. Although O. tsutsugamushi is an emerging public health threat, its pathogenic mechanisms remain markedly understudied. Bacterial pathogens subvert host actin dynamics by encoding guanine nucleotide exchange factors (GEFs) as effector proteins, which activate cellular Rho GTPases. Here, we identify a GEF domain within an O. tsutsugamushi protein that activates the host GTPase Rac1. While the overall shape of the GEF is similar to that of other bacterial effectors, the primary sequence, topology, and catalytic mechanism are completely distinct, suggesting convergent evolution. Our studies reveal a cryptic GEF domain encoded by O. tsutsugamushi and provide the groundwork to probe the role of cytoskeletal modulation in this neglected pathogen. Rho family GTPases regulate an array of cellular processes and are often modulated by pathogens to promote infection. Here, we identify a cryptic guanine nucleotide exchange factor (GEF) domain in the OtDUB protein encoded by the pathogenic bacterium Orientia tsutsugamushi. A proteomics-based OtDUB interaction screen identified numerous potential host interactors, including the Rho GTPases Rac1 and Cdc42. We discovered a domain in OtDUB with Rac1/Cdc42 GEF activity (OtDUBGEF), with higher activity toward Rac1 in vitro. While this GEF bears no obvious sequence similarity to known GEFs, crystal structures of OtDUBGEF alone (3.0 Å) and complexed with Rac1 (1.7 Å) reveal striking convergent evolution, with a unique topology, on a V-shaped bacterial GEF fold shared with other bacterial GEF domains. Structure-guided mutational analyses identified residues critical for activity and a mechanism for nucleotide displacement. Ectopic expression of OtDUB activates Rac1 preferentially in cells, and expression of the OtDUBGEF alone alters cell morphology. Cumulatively, this work reveals a bacterial GEF within the multifunctional OtDUB that co-opts host Rac1 signaling to induce changes in cytoskeletal structure.
Novel ionic liquids-based extraction method that preserves molecular structure from cutin

The biopolyester cutin is ubiquitous in land plants, building the polymeric matrix of the plant’s outermost defensive barrier - the cuticle. Cutin influences many biological processes in planta however due to its complexity and highly branched nature, the native structure remains partially unresolved. Our aim was to define an original workflow for the purification and systematic characterisation of the molecular structure of cutin. To purify cutin we tested the ionic liquids cholinium hexanoate and 1-butyl-3-methyl-imidazolium acetate. The ensuing polymers are highly esterified, amorphous and have the typical monomeric composition as demonstrated by solid state NMR, complemented by spectroscopic (GC-MS), thermal (DSC) and x-ray scattering (WAXS) analyses. A systematic study by solution-state NMR of cryogenically milled cutins extracted from Micro-Tom tomatoes (the wild type and the gpat6 and cus1 mutants) was undertaken. Their molecular structures, relative distribution of ester aliphatics, free acid end-groups and free hydroxyl groups, differentiating between those derived from primary and secondary esters, were solved. The acquired data demonstrate the existence of free hydroxyl groups in cutin and reveal novel insights on how the mutations impact the esterification arrangement of cutin. Compared to conventional approaches, the usage of ionic liquids for the study of plant polyesters opens new avenues since simple modifications can be applied to recover a biopolymer carrying distinct types/degrees of modifications (e.g. preservation of esters or cuticular polysaccharides), which in combination with the solution NMR methodologies developed here, constitutes now essential tools to fingerprint the multi-functionality and the structure of cutin in planta.
Patterns of multisensory facilitation distinguish peripersonal from reaching space

Abstract Peripersonal space is a multisensory representation of the space near body parts facilitating interactions with the close environment. Studies on non-human and human primates converge in showing that peripersonal space (PPS) is a body-part-centred representation that guides actions. Because of these characteristics, growing confusion conflates peripersonal and arm-reaching space (ARS) that is the space one’s arm can reach. Despite neuroanatomical evidence favors their distinction, whether PPS and ARS tap into different spatial representations remains poorly understood. Here, in five experiments we found that PPS differs from ARS in male and female human participants (N = 120), as evidenced both by their performance and the modeling of their multisensory facilitation. We mapped multisensory facilitation in detecting touches at the hand, placed in different locations radially within ARS. Results showed that 1) PPS is smaller than ARS; 2) multivariate modeling of spatial patterns of multisensory facilitation predicts well the position of the participants’ hand within ARS; 3) multisensory facilitation maps shift according to changes of hand position, revealing hand-centred coding of PPS, but not ARS; and 4) cross-correlation analyses highlight isomorphic multisensory facilitation maps across hand positions, suggesting their functional similarity to the receptive fields of monkeys’ multisensory neurons. In sharp contrast, ARS mapping produced undistinguishable patterns across hand positions, cross-validating the conclusion that PPS and ARS are distinct. These findings call for a refinement of theoretical models of PPS and ARS, which are relevant in constructs as diverse as action and self representation, (social) interpersonal distance, brain-machine interfaces and neuroprosthetics. Significance Statement The peripersonal space (PPS) is a multisensory interface allowing us to interact with objects in the space close to our body-parts, playing a fundamental role for the defense of the body and for the motor control of actions. Recent research has conflated PPS with the arm-reaching space (ARS), that is whole space reachable by the arm. However, there is actually no evidence supporting this equivalence and the anatomical and functional differences between PPS and ARS have been largely overlooked. In this paper, we frame the theoretical issue in depth, validate a novel methodological paradigm across five experiments, and eventually report robust and cross-validated evidence for the distinction between PPS and ARS, supported by both multivariate and univariate analyses.