Miracle-dz/UniFAR-FTUs huggingface dataset:
Muscle Microbiopsy to Delineate Stem Cell Involvement in Young Patients: A Novel Approach for Children With Cerebral Palsy

Cerebral palsy (CP), the single largest cause of childhood physical disability, is characterized firstly by a lesion in the immature brain, and secondly by musculoskeletal problems that progress with age. Previous research reported altered muscle properties, such as reduced volume and satellite cell (SC) numbers and hypertrophic extracellular matrix compared to typically developing (TD) children (>10 years). Unfortunately, data on younger CP patients are scarce and studies on SCs and other muscle stem cells in CP are insufficient or lacking. Therefore, it remains difficult to understand the early onset and trajectory of altered muscle properties in growing CP children. Because muscle stem cells are responsible for postnatal growth, repair and remodeling, multiple adult stem cell populations from young CP children could play a role in altered muscle development. To this end, new methods for studying muscle samples of young children, valid to delineate the features and to elucidate the regenerative potential of muscle tissue, are necessary. Using minimal invasive muscle microbiopsy, which was applied in young subjects under general anaesthesia for the first time, we aimed to isolate and characterize muscle stem cell-derived progenitors of TD children and patients with CP. Data of 15 CP patients, 3–9 years old, and 5 aged-matched TD children were reported. The muscle microbiopsy technique was tolerated well in all participants. Through the explant technique, we provided muscle stem cell-derived progenitors from the Medial Gastrocnemius. Via fluorescent activated cell sorting, using surface markers CD56, ALP, and PDGFRa, we obtained SC-derived progenitors, mesoangioblasts and fibro-adipogenic progenitors, respectively. Adipogenic, skeletal, and smooth muscle differentiation assays confirmed the cell identity and ability to give rise to different cell types after appropriate stimuli. Myogenic differentiation in CP SC-derived progenitors showed enhanced fusion index and altered myotube formation based on MYOSIN HEAVY CHAIN expression, as well as disorganization of nuclear spreading, which were not observed in TD myotubes. In conclusion, the microbiopsy technique allows more focused muscle research in young CP patients. Current results show altered differentiation abilities of muscle stem cell-derived progenitors and support the hypothesis of their involvement in CP-altered muscle growth.
Biochemical Prospects of Various Microbial Pectinase and Pectin: An Approachable Concept in Pharmaceutical Bioprocessing

Both pectin and pectinase are vitally imperative biomolecules in the biotechnological sector. These molecules are a feasible non-toxic contrivance of nature with extensive applicative perception. Understanding pectic substances and their structure, unique depolymerization, and biochemical properties such as a catalytic mechanism and the strong interrelationship among these molecules could immensely enhance their applicability in industries. For instance, gaining knowledge with respect to the versatile molecular heterogeneity of the compounds could be considered as the center of concern to resolve the industrial issues from multiple aspects. In the present review, an effort has been made to orchestrate the fundamental information related to structure, depolymerization characteristics, and classification of pectin as well as the types and biochemical properties of pectinase. Furthermore, various production methods related to the optimization of the product and its significant contribution to the pharmaceutical industry (either pectinase or derived pectic substances) are described in this article.
Reaching for known unknowns: Rapid reach decisions accurately reflect the future state of dynamic probabilistic information

Everyday tasks such as catching a ball appear effortless, but in fact require complex interactions and tight temporal coordination between the brain’s visual and motor systems. What makes such interceptive actions particularly impressive is the capacity of the brain to account for temporal delays in the central nervous system—a limitation that can be mitigated by making predictions about the environment as well as one’s own actions. Here, we wanted to assess how well human participants can plan an upcoming movement based on a dynamic, predictable stimulus that is not the target of action. A central stationary or rotating stimulus determined the probability that each of two potential targets would be the eventual target of a rapid reach-to-touch movement. We examined the extent to which reach movement trajectories convey internal predictions about the future state of dynamic probabilistic information conveyed by the rotating stimulus. We show that movement trajectories reflect the target probabilities determined at movement onset, suggesting that humans rapidly and accurately integrate visuospatial predictions and estimates of their own reaction times to effectively guide action.
Integrating Actin and Myosin II in a Viscous Model for Cell Migration

This article presents a mathematical and computational model for cell migration that couples a system of reaction-advection-diffusion equations describing the bio-molecular interactions between F-actin and myosin II to a force balance equation describing the structural mechanics of the actin-myosin network. In eukaryotic cells, cell migration is largely powered by a system of actin and myosin dynamics. We formulate the model equations on a two-dimensional cellular migrating evolving domain to take into account the convective and dilution terms for the biochemical reaction-diffusion equations, with hypothetically proposed reaction-kinetics. We employ the evolving finite element method to compute approximate numerical solutions of the coupled biomechanical model in two dimensions. Numerical experiments exhibit cell polarization through symmetry breaking which are driven by the F-actin and myosin II. This conceptual hypothetical proof-of-concept framework set premises for studying experimentally-driven actin-myosin reaction-kinetic network interactions with generalizations to multi-dimensions.
Population Dynamics and Economic Threshold Level of Amrasca Biguttula Biguttula Ishida in Okra

The infestation of Amrasca biguttula biguttula Ishida was started at 21 days old okra crop and reached its peak when the crop IN wasabout63 days old and thereafter its population followed declining trend. The economic threshold was determined as 2 jassids per leaf of okra. Four spraying of imidacloprid gave highest net return Rs.35,760 and cost benefit ratio 1:10.
Generation of nonhuman primate retinitis pigmentosa model by in situ knockout of RHO in rhesus macaque retina

Retinitis pigmentosa (RP) is a form of inherited retinal degenerative disease that ultimately involves the macula, which is present in primates but not in the rodents. Therefore, creating nonhuman primate (NHP) models of RP is of critical importance to study its mechanism of pathogenesis and to evaluate potential therapeutic options in the future. Here we applied adeno-associated virus (AAV)-delivered CRISPR/SaCas9 technology to knockout the RHO gene in the retinae of the adult rhesus macaque (Macaca mulatta) to investigate the hypothesis whether non-germline mutation of the RHO gene is sufficient to recapitulate RP. Through a series of studies, we were able to demonstrate successful somatic editing of the RHO gene and reduced RHO protein expression. More importantly, the mutant macaque retinae displayed clinical RP phenotypes, including photoreceptor degeneration, retinal thinning, abnormal rod subcellular structures, and reduced photoresponse. Therefore, we suggest somatic editing of the RHO gene is able to phenocopy RP, and the reduced time span in generating NHP mutant accelerates RP research and expands the utility of NHP model for human disease study.
Operative choice for colon and rectal cancer: what matters?

Thearticle entitled “ Long - term outcomes of robot - assisted surgeryin patients with colorectal cancer ”, published in the Annals of SurgicalOncology , is a timely analysis of oncologic outcomes comparing robotic andconventional laparoscopic techniques (1). Several other studies have demonstratedequivalent short-term outcomes between robotic and laparoscopic groups,including postoperative complications and hospital length of stay (2-5). However, long-term oncologic outcomes for the robotic approach have not yetbeen well evaluated.
Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat

Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch), Fusarium crown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot, Fusarium crown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.
Cardiac Cell-Derived Matrices Impart Age-Specific Functional Properties to Human Cardiomyocytes

Cell-derived matrices (CDMs) isolated from cultured cells provide complex and tissue-specific biochemical and physical cues derived from the extracellular matrix (ECM) that are lacking in typical tissue culture environments. However, current methods enhance ECM adhesion and thickness via introduction and promotion of singular matrix proteins, skewing the matrix composition, and confounding comparisons between CDMs. Here we developed a protocol that enhances CDM stability and deposition, respectively, by combining an L-polydopamine surface coating with Ficoll macromolecular crowing prior to hypotonic decellularization. This methodology was applied to the study of age-dependent phenotypic and functional changes observed in cardiac ECM by comparing the morphologic, electrophysiological and metabolic response of cardiomyocytes in response to CDMs produced by fetal and adult cardiac fibroblasts. Furthermore, mass spectrometry proteomics identified the enrichment of collagen VI in fetal CDMs, which we determined via siRNA-mediated silencing during CDM production to be necessary for maximal oxidative respiration in cardiomyocytes.
Optimization of epothilone B production by Sorangium cellulosum using multiple steps of the response surface methodology

The anticancer compound epothilone B is biosynthesized by the myxobacteriumSorangium cellulosum; however, the fermentation characteristics for epothilone production in Sorangium cellulosum have not yet been reported. In this study, medium components for the production of epothilone B in the So0157-2 strain of S. cellulosum were statistically screened and optimized. First, the nutrients in the fermentation medium were optimized in one-factor-at-a-time, Plackett–Burman design, and Box–Behnken design experiments. Afterwards, three nutritional parameters were selected for the optimization of epothilone B production in shaking flask cultures using a central composite response surface methodology design; a polynomial equation model that related the medium components and epothilone B yield was established. The data were further analyzed using response surface plots and canonical mathematical model analyses with the SAS 8.0 software. After optimized, the yield of epothilone B increased to 82.0 ± 3 mg/l, 7.2-fold higher than the initial yield (11.3 ± 0.4 mg/l). Key words: Myxobacterium, Sorangium cellulosum, epothilone B, statistical optimization, response surface methodology.
Mechanism of duplex unwinding by coronavirus nsp13 helicases

The current COVID-19 pandemic urges in-depth investigation into proteins encoded with coronavirus (CoV), especially conserved CoV replicases. The nsp13 of highly pathogenic MERS-CoV, SARS-CoV-2, and SARS-CoV exhibit the most conserved CoV replicases. Using single-molecule FRET, we observed that MERS-CoV nsp13 unwound DNA in discrete steps of approximately 9 bp when ATP was used. If another NTP was used, then the steps were only 4 to 5 bp. In dwell time analysis, we detected 3 or 4 hidden steps in each unwinding process, which indicated the hydrolysis of 3 or 4 dTTP. Based on crystallographic and biochemical studies of CoV nsp13 helicases, we modeled an unwinding mechanism similar to the spring-loaded mechanism of HCV NS3 helicase, although our model proposes that flexible 1B and stalk domains, by allowing a lag greater than 4 bp during unwinding, cause the accumulated tension on the nsp13-DNA complex. The hinge region between two RecA-like domains in SARS-CoV-2 nsp13 is intrinsically more flexible than in MERS-CoV nsp13 due to the difference of a single amino acid, which causes the former to induce significantly greater NTP hydrolysis. Our findings thus establish a blueprint for determining the unwinding mechanism of a unique helicase family. When dTTP was used as the energy source, 4 hidden steps in each individual unwinding step after 3 - 4 NTP hydrolysis were observed. An unwinding model of MERS-CoV-nsp13 which is similar to the spring-loaded mechanism of HCV NS3 helicase, except the accumulation of tension on nsp13/DNA complex is caused by the flexible 1B and stalk domains that allow a lag of 4-bp in unwinding. Comparing to MERS-CoV nsp13, the hinge region between two RecA-like domains in SARS-CoV-2 nsp13 is intrinsically more flexible due to a single amino acid difference, which contributes to the significantly higher NTP hydrolysis by SARS-CoV-2 nsp13.
Genetic structure of tautog (Tautoga onitis) populations assayed by RFLP and DGGE analysis of mitochondrial and nuclear genes

The tautog (Tautoga onitis) is one of two temperate labrid species commonly inhabiting the coastal marine and estuarine waters of the mid-Atlantic coast of the United States. Although the species range extends from the outer coast of Nova Scotia to Georgia, tautog are most abundant from Cape Cod to Chesa- peake Bay (Bigelow and Schroeder, 1953). They are generally found in high relief, reefl ike habitats such as those associated with jetties, break- Abstract. -The tautog (Tautoga onitis) is one of two temperate labrid species commonly inhabiting the coastal marine and estuarine waters of the mid-Atlan- tic coast of the United States. To delin- eate population structure throughout its primary range, we examined samples collected from three sites (Rhode Island, Delaware, Virginia). Five regions of the mitochondrial genome (COI, ATPase 6, cyt b, ND2 and control region) and one nuclear intron were amplifi ed by PCR and screened for sequence variation with a battery of restriction enzymes (RFLP analysis), or by denaturing gra- dient gel electrophoresis (DGGE). With RFLP analysis an average of 129 restriction sites per individual were revealed and 532 bases per individual were surveyed. Polymorphisms were observed in the ND2 and control region fragments, but not in the COI, ATPase 6, or cyt b fragments. Mean within- sample haplotype diversity was 0.6905 (±0.00184), within the range of values reported for other marine species. How- ever, mean nucleotide diversity was 0.000782, one of the lowest values re- ported for a marine teleost. Corrected nucleotide divergence between samples was essentially zero, suggesting the absence of population structuring along the mid-Atlantic Coast. DGGE analy- ses of COI, cyt b, and a lactate dehy- drogenase (LDH) intron revealed little additional variation; each product pos- sessed a single common haplotype and occasional rare variants. The low level of genetic diversity ob- served in the tautog may refl ect a small effective population size resulting from historical population bottlenecks or large variance in reproductive success. The apparent absence of geographic differen- tiation suggests that tautog from Rhode Island to Virginia form a single genetic stock; data from additional genetic poly- morphisms are needed to confi rm or dis- prove this conclusion.
Ultraviolet crown coloration in female blue tits predicts reproductive success and baseline corticosterone

A growing number of studies provide evidence that female plumage coloration is indicative of individual quality and can influence male mate choice. In blue tits (Cyanistes caeruleus), both sexes exhibit bright ultraviolet (UV)-reflectant crown feathers, which have previously been shown to be attractive to the opposite sex. In males, there is evidence that UV reflectance of the crown feathers is an honest signal of quality in this species, but it is unclear whether this is the case for females. To address this, the UV signal (an index of relative UV reflectance specific to the visual sensitivities of the blue tit) of mothers was measured during brood rearing for 3 years (2008–2010) and related to indices of reproductive success, that is, lay date, clutch size, and number of chicks fledged and maternal state, that is, body condition and baseline corticosterone (CORT). Maternal UV signal was unrelated to clutch size but was positively correlated with number of chicks fledged in 3 years. Maternal UV signal was also negatively correlated with lay date, but this was not consistent across years. In addition, maternal UV signal was negatively correlated with baseline CORT in all years but was not predictive of body condition. Taken together, these results provide evidence that female plumage coloration is indicative of female quality and may serve as a signal for mate choice. Further, it provides novel evidence that maternal baseline CORT is associated with UV plumage signal in free-living birds and may be an important mechanistic link between an individual’s ornamentation, state, and reproductive performance.
Multi-scale modeling of macrophage – T cell interactions within the tumor microenvironment and impacts of macrophage-based immunotherapies

Within the tumor microenvironment, macrophages exist in an immunosuppressive state, preventing T cells from eliminating the tumor. Due to this, research is focusing on immunotherapies that specifically target macrophages in order to reduce their immunosuppressive capabilities and promote T cell function. In this study, we develop an agent-based model consisting of the interactions between macrophages, T cells, and tumor cells to determine how the immune response changes due to three macrophage-based immunotherapeutic strategies: macrophage depletion, recruitment inhibition, and macrophage reeducation. We find that reeducation, which converts the macrophages into an immune promoting phenotype, is the most effective strategy and that the macrophage recruitment rate and tumor proliferation rate (tumor-specific properties) have large impacts on therapy efficacy. We also employ a novel method of using a neural network to reduce the computational complexity of an intracellular signaling mechanistic model.
Overview of General and Discriminating Markers of Differential Microglia Phenotypes

Inflammatory processes and microglia activation accompany most of the pathophysiological diseases in the central nervous system. It is proven that glial pathology precedes and even drives the development of multiple neurodegenerative conditions. A growing number of studies point out the importance of microglia in brain development as well as in physiological functioning. These resident brain immune cells are divergent from the peripherally infiltrated macrophages, but their precise in situ discrimination is surprisingly difficult. Microglial heterogeneity in the brain is especially visible in their morphology and cell density in particular brain structures but also in the expression of cellular markers. This often determines their role in physiology or pathology of brain functioning. The species differences between rodent and human markers add complexity to the whole picture. Furthermore, due to activation, microglia show a broad spectrum of phenotypes ranging from the pro-inflammatory, potentially cytotoxic M1 to the anti-inflammatory, scavenging, and regenerative M2. A precise distinction of specific phenotypes is nowadays essential to study microglial functions and tissue state in such a quickly changing environment. Due to the overwhelming amount of data on multiple sets of markers that is available for such studies, the choice of appropriate markers is a scientific challenge. This review gathers, classifies, and describes known and recently discovered protein markers expressed by microglial cells in their different phenotypes. The presented microglia markers include qualitative and semi-quantitative, general and specific, surface and intracellular proteins, as well as secreted molecules. The information provided here creates a comprehensive and practical guide through the current knowledge and will facilitate the choosing of proper, more specific markers for detailed studies on microglia and neuroinflammatory mechanisms in various physiological as well as pathological conditions. Both basic research and clinical medicine need clearly described and validated molecular markers of microglia phenotype, which are essential in diagnostics, treatment, and prevention of diseases engaging glia activation.
Returning Samples From Enceladus for Life Detection

Evidence suggests that Saturn's icy moon Enceladus has a subsurface ocean that sources plumes of water vapor and ice vented to space from its south pole. In situ analyses of this material by the Cassini spacecraft have shown that the ocean contains key ingredients for life (elements H, C, N, O and possibly S; simple and complex organic compounds; chemical disequilibria at water-rock interfaces; clement temperature, pressure, and pH). The Cassini discoveries make Enceladus' interior a prime locale for life detection beyond Earth. Scant material exchange with the inner Solar System makes it likely that such life would have emerged independently of life on Earth. Thus, its discovery would illuminate life's universal characteristics. The alternative result of an upper bound on a detectable biosphere in an otherwise habitable environment would likewise considerably advance our understanding of the prevalence of life beyond Earth. Here we outline the rationale for returning vented ocean samples, accessible from Enceladus' surface or low altitudes, to Earth for life detection. Returning samples allows analyses using laboratory instruments that cannot be flown, with decades or more to adapt and repeat analyses. We describe an example set of measurements to estimate the amount of sample to be returned and discuss possible mission architectures and collection approaches. We then turn to the challenges of preserving sample integrity and implementing planetary protection policy. We conclude by placing such a mission in the broader context of Solar System exploration.