Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Bacillus subtilis Penicillin-Binding Protein PBP4

Purpose: The PBP4* is a Penicillin Binding Protein belonging to the class C of AmpH type whose function remains poorly understood. This study aimed to evaluate the biophysical and enzymatic properties of the Bacillus subtilis PBP4* to gain insights into its role in the context of bacterial cell wall recycling. Methods: To characterize the PBP4*, the full-length PBP4* and its N-terminal penicillin-binding domain have been produced in Escherichia coli and purified. Results: A comparison of biophysical properties has shown that both recombinant proteins are monomeric in solution and retain the same thermal stability. On the other hand, the D-alanine methyl esterase activity detected with the full-length PBP4* is impeded by the cleavage of the 92 amino acid C-terminal domain. The esterase activity of the full-length PBP4* strates a clear D-stereospecificity. The PBP4* is also active on B. subtilis cell walls bearing teichoic acids, compounds commonly substituted with D-alanine residues. Conclusions: Our results are in agreement with the hypothesis that PBP4* could play a role in recycling cell wall components, as previously suggested.
Low concordance of short‐term and long‐term selection responses in experimental Drosophila populations

Experimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study in Drosophila simulans to compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10% of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.
Plant richness, turnover, and evolutionary diversity track gradients of stability and ecological opportunity in a megadiversity center

Significance What explains global patterns of diversity—environmental history or ecology? Most studies have focused on latitudinal gradients—the decline of diversity from the tropics to the poles. A problem with this is that it conflates predictions of historical and ecological hypotheses: The productive tropics have also experienced high Cenozoic biome stability. Longitudinal diversity gradients can overcome this constraint. We use a longitudinal diversity gradient in the megadiverse Cape Floristic Region to model species and evolutionary diversity in terms of Pleistocene climate stability and ecological heterogeneity. We find that biome stability is the strongest predictor of diversity measures, and argue that stability, in conjunction with measures of ecological opportunity—other than productivity—may provide a general explanation for global diversity patterns. Research on global patterns of diversity has been dominated by studies seeking explanations for the equator-to-poles decline in richness of most groups of organisms, namely the latitudinal diversity gradient. A problem with this gradient is that it conflates two key explanations, namely biome stability (age and area) and productivity (ecological opportunity). Investigating longitudinal gradients in diversity can overcome this problem. Here we investigate a longitudinal gradient in plant diversity in the megadiverse Cape Floristic Region (CFR). We test predictions of the age and area and ecological opportunity hypotheses using metrics for both taxonomic and phylogenetic diversity and turnover. Our plant dataset includes modeled occurrences for 4,813 species and dated molecular phylogenies for 21 clades endemic to the CFR. Climate and biome stability were quantified over the past 140,000 y for testing the age and area hypothesis, and measures of topographic diversity, rainfall seasonality, and productivity were used to test the ecological opportunity hypothesis. Results from our spatial regression models showed biome stability, rainfall seasonality, and topographic heterogeneity were the strongest predictors of taxonomic diversity. Biome stability alone was the strongest predictor of all diversity metrics, and productivity played only a marginal role. We argue that age and area in conjunction with non–productivity-based measures of ecological opportunity explain the CFR’s longitudinal diversity gradient. We suggest that this model may possibly be a general explanation for global diversity patterns, unconstrained as it is by the collinearities underpinning the latitudinal diversity gradient.
Site‐specific metastasis: A cooperation between cancer cells and the metastatic microenvironment

The conclusion derived from the information provided in this review is that disseminating tumor cells (DTC) collaborate with the microenvironment of a future metastatic organ site in the establishment of organ‐specific metastasis. We review the basic principles of site‐specific metastasis and the contribution of the cross talk between DTC and the microenvironment of metastatic sites (metastatic microenvironment [MME]) to the establishment of the organ‐specific premetastatic niche; the targeted migration of DTC to the endothelium of the future organ‐specific metastasis; the transmigration of DTC to this site and the seeding and colonization of DTC in their future MME. We also discuss the role played by DTC‐MME interactions on tumor dormancy and on the differential response of tumor cells residing in different MMEs to antitumor therapy. Finally, we summarize some studies dealing with the effects of the MME on a unique site‐specific metastasis—brain metastasis.
Meat Quality Parameters and Sensory Properties of One High-Performing and Two Local Chicken Breeds Fed with Vicia faba

The current practices of the poultry industry have raised concerns among consumers. Among these is the culling of day-old male chicks of laying hybrids; a suitable alternative for this could be the use of dual-purpose breeds where both sexes are used. Another practice that causes concern is the import of large quantities of soybeans for feedstuff production. Substitutes for these soybean-based products are regional protein crops, such as faba beans (Vicia faba L.; FBs). The objective of this study was to test the suitability of FB as a locally produced soybean meal replacement for two local dual-purpose chicken breeds and one high-performing layer line. The breast and leg meat of male Bresse Gauloise (BG), Vorwerkhuhn (VH), and White Rock (WR) animals was evaluated for different meat quality parameters: pH, color, water holding capacity, and tenderness. Sensory properties of the samples were evaluated by a trained panel with a conventional descriptive analysis. Results show different effects of FB diets on meat quality parameters in the different breeds. The attributes mostly affected by the diet are related to aroma, flavor, and texture, particularly in VH and WR. Overall, faba beans appear to be an acceptable dietary protein source for rearing these breeds for meat production.
Human Cytomegalovirus Circumvents NF-κB Dependence in Retinal Pigment Epithelial Cells1

The human CMV (HCMV) is a persistent virus that may cause severe inflammatory responses especially in immunocompromised hosts. In different cell types, HCMV infection leads to the activation of the pleiotropic transcription factor, NF-κB, which triggers virus replication but also propagates cell-mediated inflammatory mechanisms that largely depend on PG synthesis. We investigated the interactions of HCMV and the NF-κB-dependent PG synthesis pathway in cultures of retinal pigment epithelial (RPE) cells that are known to be infected in HCMV retinitis patients. Unlike in other cell types, HCMV increased neither NF-κB activity nor p65 and p105/50 mRNA levels in RPE cells. Both TNF-α and phorbol ester 12,0-tetradecanoylphorbol 13-acetate (TPA) enhanced NF-κB activity but only TPA increased HCMV replication. Cyclooxygenase-2 expression and PGE2 release was increased by TPA and TNF-α but not by HCMV infection. Stimulatory activity of TPA on HCMV replication was suppressed by protein kinase C inhibitors and inhibitors of p42/44 and p38 mitogen-activated protein kinases but not by NF-κB inhibitors. In conclusion, HCMV circumvents the NF-κB route in favor of the protein kinase C-dependent mitogen-activated protein kinase pathway in RPE cells. This virus/host cell interaction might be a mechanism that promotes HCMV persistence in immune-privileged organs such as the eye.
Is the Agricultural Work a Risk Factor for Koreans Elderly Spinal Sagittal Imbalance?

Objective A primary degenerative sagittal imbalance has been considered because of unique lifestyles such as the prolonged crouched posture during agricultural work and performing activities of daily living on the floor. Previous papers have reported that sagittal imbalance disease is often seen distinctly in the farming districts of “oriental” countries such as Korea and Japan. However, this finding was only evaluated with the use of X-ray, and other factors such as magnetic resonance imaging (MRI), muscle volume, compression fracture, and laboratory results were not considered. Thus, using these, we evaluate the agricultural work-associated factors for Korean elderly spinal sagittal imbalance. Methods We recruited 103 Korean participants who had a sagittal vertical axis (SVA) of >5 cm in this Korean Elderly Sagittal Imbalance Cohort Study. The following were evaluated : radiological parameters, MRI, compression fracture, vitamin D, parathyroid hormone, C-terminal telopeptide, osteocalcin, bone mineral density and muscle fatty change, muscle volume, and health-related quality of life from patients’ survey. Moreover, in this survey, the farmers’ annual working hours were investigated. Subsequently, we analyzed the associated factors for spinal sagittal imbalance depending on occupation. Results A total of 46 participants were farmers, and the others were housewives, sellers, and office workers. The farmer group had more SVA (141 vs. 99 mm, p=0.001) and pelvic tilt (31° vs. 24°, p=0.004) and lesser lumbar lordosis (20° vs. 30°, p=0.009) and thoracic kyphosis (24° vs. 33°, p=0.03) than non-farmer group. A significantly positive correlation was noted between the working hour and SVA in the farmer group (p=0.014). The visual analogue scale score for back pain (8.26 vs. 6.96, p=0.008) and Oswestry Disability Index (23.5 vs. 19.1, p=0.003) in the farmer group were higher than that in the non-farmer group, but the Short Form-36 score was not significantly different between the two groups. The Mini-Mental State Exam score was significantly lower in the farmer group than in the non-farmer group (24.85 vs. 26.98, p=0.002). Conclusion The farmer group had more sagittal imbalance and back pain in proportion to the working hours even though the muscle and bone factors and general laboratory condition were not significantly different between the two groups. These results supported that the long hours spent in the crouched posture while performing agricultural work were a risk factor for severe sagittal imbalance.
What Factors Shape Self-Reported Health Among Community-Dwelling Older Adults? A Scoping Review

ABSTRACT Self-reported health is a predictive measure of morbidity and mortality across populations. A comprehensive understanding of the factors that shape self-reported health among community-dwelling older adults, a growing population globally, is lacking. The aim of this review was to summarize the factors that are associated with self-reported health among this population and identify key areas for future research. Accordingly, we conducted a scoping review using the stage-wise framework developed by Arksey and O’Malley. We summarized 42 factors, as identified in 30 publications, and organized them into four categories. Key factors shaping self-reported health included the presence of chronic conditions and depressive symptoms. As the population of community-dwelling older adults continues to increase, there remains a need to understand how these identified factors shape self-reported health. To date, empirical research has been limited to observational and cross-sectional designs. There is a need to further explore these factors in longitudinal data.
Comparative Study of MLH and SAM Classification Techniques using Multispectral Data of EO-1 Satellite

This paper presents a case study on classification of multispectral image in the Kajali Dongari near Meghnagar Jhabua Distt. Madhya Pradesh. The purpose of this research study is to find the feasible technique for mapping of research area. Preprocessing of ALI sensor of Earth observing 1(EO 1) satellite data is required for conversion from digital value to reflectance. MNF and PPI method is used for endmember fraction. For vegetation endmember fraction can be easily extracted by NDVI image. Maximum LikeHood (MLH) and Spectral Angle Mapper (SAM) techniques are used for classification. Finally study area is classified in five feature namely natural rocks, exploited rock, vegetation, soil, and water. After analysis of results, Research area would be classified with better accuracy by SAM technique and area of rock is 55.827%, exploited rock is 12.106%, water is 0.841%, vegetation is 11.564% and soil is 19.685% of total area of research field.
Genetic study of cognitive function

textabstractDissecting the genetics of Alzheimer’s disease (AD) and Parkinson’s disease (PD) has contributed significantly to our understanding of the pathogenesis of neurodegeneration in these two complex disorders. For AD, three highly penetrant genes (APP, PSEN1 and PSEN2) and one susceptibility gene (APOE) have been identified. For PD, seven genes (SNCA, Parkin, UCHL1, NR4A2, DJ1, PINK1 and LRRK2) have been found. These genes explain only a small proportion of AD and PD patients and are mostly associated with an early onset presentation of the disease. APOE remains the only common gene, which increases the risk of both rare early and late onset AD. The ongoing challenge is to unravel the genetics of the most frequent forms of these complex disorders. In the present paper, we briefl y review the state of the art in the genetics of AD and PD. We also discuss the prospects of finding new genes associated with common forms of these diseases in light of two hypotheses concerning the genetic variation of complex diseases: common disease/ common variants and common disease/rare variants.
Study of Metallo-Beta-Lactamase Producing Gram Negative Bacteria in a Tertiary Care Hospital

Resistant bacteria are emerging worldwide as a threat to the favorable outcome of common infection in community & hospital settings. Beta-lactams remain a cornerstone for antimicrobial chemotherapy of a large number of bacterial infections. The most common cause of bacterial resistance to βlactam antibiotics is the production of βlactamases, followed by ESBL’s and then the emergence of MBL activity which is one of the most feared resistance mechanism, because of its ability to hydrolyze virtually all βlactams, including cabapenems. However MBL’s are unable to hydrolyze monobactams & are not inactivated by βlactamase inhibitors like clavulinic acid, sulbactam and Tazobactam. In any nosocomial settings, carbapenems are used as the last resort for treatment of MDR gram negative bacterial infections. MBL producing gram negative bacteria often exhibit resistance to additional classes of drugs and behave as multidrug resistant bacteria. Hence the present study was undertaken for detection of MBL producing gram negative bacilli and to help treating physicians to select appropriate antibiotic in our hospital. It was a prospective study conducted from April 2018 to July 2018 after IEC clearance. The Gram Negative isolates were first screened for MBL production with ceftazidime disc, & were further tested by Combined Disc Test Method (CDT) and Modified Hodge Test (MHT). Total 300 gram negative isolates were studied. In these, the MBL producers were 43.6%, majority of the isolates were from pus (19.3%), followed by urine (14.3%). Amongst these, E. coli was the most common organism isolated (16.3%), followed by Klebsiella pneumoniae(11%) and Pseudomonas aeruginosa (6.6%). By combined disc test a total of 131 MBL producing strains were isolated and 126 strains were detected by MHT. The exposure of bacterial strains to a multitude of βlactams has induced mutation of βlactamase in many bacteria, expanding their activity even against carbapenems, by the production of MBL resulting into fewer therapeutic alternatives. Hence detection of MBL is very important in respect to the treatment plan and sparing use of antibiotics to avoid their spread in the hospitals.
Unregulated Trade in Turtle Shells for Chinese Traditional Medicine in East and Southeast Asia: The Case of Taiwan

Abstract Based on customs trade statistics from 1999 to 2008, a total of 1989 metric tons of shells of hard-shelled chelonians have been imported into Taiwan for consumption in the traditional Chinese medicine (TCM) market, with an average of 198.9 metric tons/y. The total amount of soft-shell turtle shells imported was 290 metric tons, averaging 29.0 metric tons/y. This volume indicates that millions of turtles and tortoises have been killed annually for the TCM market in Taiwan alone. The trade of turtle shells for TCM has existed in huge volumes for a long time, with no significant decrease in the market size through Convention on International Trade in Endangered Species of Wild Fauna and Flora listing of the main target species. Although the customs trade records were not species-specific, in the market survey conducted in 1996–2002, a total of 39 species of turtles and tortoises, mainly originating from China, Southeast and South Asia, were identified. Only 3 non-Asian species were found. The larger number and numerous species of origin in turtle-shell trade for the TCM market indicate blatant disregard by traders for law and authority of responsible agencies from both source and consumer countries. Observed levels of usage and trade of turtle shells appear to be highly unsustainable and may have a great impact on the chelonian fauna in source areas. For the sustainability of chelonian fauna in Asia, clear policies and close international cooperation for the regulation of turtle-shell trade are urgently needed.
Habitat preference reflects social organization of humpback whales (Megaptera novaeangliae) on a wintering ground

Habitat preference is driven by a complex interaction among behavioural patterns, biological requirements, and environmental conditions. These variables are difficult to determine for any species but are further complicated for migratory marine mammals, such as humpback whales Megaptera novaeangliae . Patterns of habitat use in relation to social organization potentially exist for this species on their wintering grounds. Using an integrated GIS approach, we examined the degree to which spatial patterns of habitat stratification are correlated within different humpback whale group types from 6 years of sighting data (1996–2001) collected on the Antongil Bay, Madagascar, wintering ground. Stratification of humpback whale sightings by behavioural classification showed significant variation in depth and distance from shore. Distribution by depth could not be described as a function of group size but could be described as a function of social organization, with mother–calf pairs showing a strong preference for shallower water compared to all other group types. Group size and social organization seem to be factors in distribution by distance from shore. Significant diurnal patterns in distribution by depth and distance from shore also exist, where mother–calf groups maintain a relatively stable distribution and pairs and competitive groups are the most variable. Patterns of habitat preference on this wintering ground appear to be guided by social organization, where distribution by depth and distance from shore highlight areas critical to conservation.
Exploiting physical defence traits for crop protection: leaf trichomes of Rubus idaeus have deterrent effects on spider mites but not aphids

Plants possess anti-herbivore defences that could be exploited for crop protection. The potential for deploying physical defence traits for more sustainable pest management (i.e. reduced pesticide application) has not been fully realised. Using a perennial crop (red raspberry, Rubus idaeus), we take the novel approach of quantifying within- and between-genotype variation in a resistance trait, leaf trichome density, to determine precisely the effect of trichomes on host plant preference and suitability for two shoot-feeding arthropods, the European large raspberry aphid (Amphorophora idaei) and two-spotted spider mite (Tetranychus urticae). Additionally, we tested whether this trait influenced searching behaviour of a generalist herbivore predator (lacewing larvae, Chrysoperla carnea). Although there was no consistent genotypic variation in R. idaeus suitability for T. urticae, our hypothesis that T. urticae would avoid high leaf trichome density was supported on certain genotypes. The deterrent effect was mainly on egg deposition rather than leaf selection by adults, with up to sixfold differences in leaf preference depending on the genotypes offered. By contrast, there was significant genotypic variation in R. idaeus suitability for A. idaei (10-fold variation in aphid abundance), but, contrary to our prediction, aphid preference and infestation levels were unrelated to leaf trichome density. Instead, A. idaei performed best on vigorous genotypes, indicating that plant tolerance traits contributed to R. idaeus suitability for aphids. Leaf trichomes had little effect on the behaviour of the beneficial control agent C. carnea larvae. We conclude that physical anti-herbivore defences, specifically leaf trichomes, could be deployed to deter particular arthropod pests. However, the mechanistic approach adopted here is necessary to avoid antagonistic effects on other pests or on natural enemies.
Effect of Vegetation Management on Bird Habitat in Riparian Buffer Zones

Abstract Riparian buffers can be valuable refuge areas for wildlife in otherwise homogeneous agricultural landscapes. Government sponsored programs like the Cropland Reserve Program generally require the planting of specific vegetative species during buffer restoration, although the effectiveness of such an approach when compared to restoration by volunteer species is unknown. We studied the effect of differences in vegetation structure on avian habitat in riparian buffer zones. A 25 m (82 ft) wide planted woodland buffer, 30 m (98 ft) wide grass, shrub, and woodland three-zone buffer, and a 9 m (30 ft) wide shrub buffer were evaluated for habitat potential using breeding-bird counts and vegetation surveys. Bird density and species richness varied with the structure of the vegetative communities present at the three sites. Avian species richness and total detections were higher in the three-zone buffer than in both the shrub and planted buffer, likely a result of the diversity of vegetation at the site. These data suggest that restoration of riparian areas by allowing fallow vegetation to recolonize is at the very least equally beneficial to avian wildlife as is restoration by planting specific grass, shrub, and tree species. Buffer restoration by natural revegetation using this method could be recommended as an alternative to implementation by planting riparian species due to its simplicity and cost effectiveness.