Miracle-dz/UniFAR-FTUs huggingface dataset:
SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method.

Pakistani camels have been classified socio-geographically into 20 breeds, but they have not yet been subjected to substantial selective pressures and the genetic basis for these breeds is not understood. However, it should be possible to distinguish them by use of molecular data. This study investigated the genetic diversity and population structure within and between two major Pakistani camel breeds, Marecha and Lassi. As no SNP array is currently available, we first identified 63 619 SNPs using a genotyping by sequencing approach. After quality control, a panel of 36 926 SNPs was used in the analysis. Population structure was investigated with a principal coordinate analysis as well as a cluster analysis using NetView, and multilocus heterozygosity analysis to explore between- and within-breed genetic variation. In addition, between-breed variation was explored using the fixation index, FST . We also compared relationship matrices computed using the VanRaden SNP-based method and a method developed specifically for genotyping by sequencing data. Among the two camel breeds, Lassi showed a lower level of genetic diversity whereas Marecha showed a higher level. As a genotyping platform has not yet been developed for the camel, the SNPs discovered in this study will be useful in future genetic studies in camels.
Speckle tracking echocardiography in hypokinetic non‐dilated cardiomyopathy: comparison with dilated cardiomyopathy

Hypokinetic non‐dilated cardiomyopathy (HNDC), which is determined by impaired left ventricular (LV) systolic function despite normal LV size, has been categorized as a subgroup of dilated cardiomyopathy (DCM) spectrum. Lack of data regarding advanced echocardiographic data in this population motivated us to design the present study in order to assess LV myocardial deformation properties of HNDC patients against the ones with dilated left ventricle.
Gene Copy Number Quantification of SHOX, VAMP7, and SRY for the Detection of Sex Chromosome Aneuploidies in Neonates.

Aims: To explore the feasibility of detecting sex chromosome aneuploidies (SCAs) by means of gene copy number quantification of short stature homeobox (SHOX), vesicle-associated membrane protein 7 (VAMP7), and SRY in newborns. Materials and Methods: Gene doses of SHOX, VAMP7, and SRY were determined by quantitative polymerase chain reaction (qPCR) using DNA obtained from dried blood samples from newborns. Relative quantification values were obtained. An aneuploidy profile was established according to cutoff values. Samples with ≥2 gene doses (out of range) were reanalyzed, and those with aneuploidy profiles were confirmed by karyotyping. Sensitivity, specificity, and positive and negative predictive values were obtained. Results: A total of 10,033 samples were collected (4945 females and 5088 males). Of 244 (2.43%) samples with ≥2 gene doses that were retested, 20 cases were confirmed. The overall incidence of SCAs was 1 in 500 live newborns. There were six cases of Turner syndrome (1/824), 3 cases of XXX (1/1648), 7 cases of Klinefelter syndrome (1/726), and 4 cases of of XYY (1/1272). The sensitivity was 0.952 (95.24%), specificity of 0.975 (97.56%), positive predictive value of 0.909 (90.91%), and negative predictive value of 0.987 (98.77%). Conclusions: Gene copy number analyses of VAMP7, SHOX, and SRY genes by qPCR from blood samples spotted onto filter paper is a highly reliable method for the early detection of male and female SCAs.
THBS4 silencing regulates the cancer stem cell‐like properties in prostate cancer via blocking the PI3K/Akt pathway

Although thrombospondins 4 (THBS4) participates in controlling the biology of prostate cancer (PCa), the mechanism underlying this regulation remains unknown. Hence, this study aims to identify the regulatory effects of THBS4 on the PCa stem cell‐like properties and the potential mechanism associated with the phosphatidylinositol 3′‐kinase (PI3K)/protein kinase B (Akt) pathway.
Surface Morphology Formation of Edible Holographic Marker on Potato Starch with Gelatin or Agar Thin Coatings

Edible films and coatings based on biopolymers to protect and extend the shelf life of food and medicine can be functionalized, by applying a holographic marker on the coating surface for marking products or sensing storage conditions. In this work, holographic markers were prepared on the surface of thin biopolymer coatings based on starch, gelatin, agar and also starch/gelatin and starch/agar blends by the nanoimprint method from a film-forming solution. The morphology of the surface of holographic markers using optical microscopy in reflection mode was examined, as well as the reasons for its formation using an analysis of the flow curves of film-forming solutions. It was found that the surface morphology of the marker strongly depends on the composition, consistency index of film-forming solution and miscibility of the components. It was shown that the starch/agar film-forming solution at the ratio of 70/30 wt. % has a low consistency index value of 21.38 Pa·s0.88, compared to 64.56 Pa·s0.67 for pure starch at a drying temperature of 30 °C, and the components are well compatible. Thus, an isotropic morphology of the holographic marker surface was formed and the value of diffraction efficiency of 3% was achieved, compared to 1.5% for the marker made of pure starch. Coatings without holographic markers were analyzed by tensile strength and water contact angle, and their properties are highly dependent on their composition.
Life history of the amphidromous shrimp Caridina leucosticta (Decapoda: Caridea: Atyidae) in the Isazu River, Japan

The life cycle of a freshwater amphidromous shrimp Caridina leucosticta Stimpson, 1860 was studied in a temperate river from October 2005 to November 2006, including all aspects of its growth and reproduction, larval drift, distribution of developing larvae, and recruitment of developed juveniles. The growth rate of C. leucosticta was generally low when the water temperature decreased between October 2005 and April 2006. The growth rate then increased from April 2006 as the water temperature rose. Females grew faster and reached a larger body size at a given age than males. Brooding females occurred from June to September 2006. Larvae hatched in freshwater habitats were observed to flow downstream from July to October 2006, with a peak in July and August. Developing larvae were collected in September 2006, at two stations 0.6 and 2.0 km offshore from the river mouth, but were not found in the brackish estuary of the river. Developed juveniles were observed in the uppermost part of the brackish river estuary from August to November 2006. Juveniles were found in the freshwater habitat from October 2005 to April 2006 and from August to November 2006. Longevity was estimated to be 15-25 months. The life history of C. leucosticta as illustrated in the present study indicates that this species uses a broad range of habitats from fresh water to marine. Conservation measures should be considered for each habitat corresponding to each developmental stage and should also allow for connectivity between these habitats.
Chilling Tolerance of Wheat Seedlings Is Related to an Enhanced Alternative Respiratory Pathway

Pretreatment with exogenous hydrogen peroxide (H 2 O 2 ) mitigated the water loss of wheat leaves exposed to 4°C for 24 h. The same treatment also partially reduced the increases of electrolyte leakage and H 2 O 2 production of the chilled plants. These observations suggest that H 2 O 2 pretreatment could effectively induce chilling tolerance. The capacity of the alternative respiratory pathway and the expression of the gene encoding the alternative oxidase (AOX1) were substantially elevated by H 2 O 2 treatment under either normal or chilling conditions. Sali-cylhydroxamic acid (SHAM, an inhibitor of the alternative respiratory pathway) decreased the tolerance of plants to chilling conditions and reversed the chilling tolerance induced by exogenous application of H 2 O 2 These observations indicate that the tolerance of plants to chilling might be related to an enhanced alternative respiratory pathway.
Edaphic, Nutritive, and Species Assemblage Differences between Hotspots and Matrix Vegetation: Two African Case Studies

Areas of locally intense and frequent grazing, or ‘hotspots’, are pervasive features in tropical grasslands and savannas. In some ecosystems, hotspot presence is clearly associated with edaphic factors (e.g., high clay content and elevated soil fertility), such as those that develop in abandoned cattle bomas. Studies in a range of other savanna ecosystems, however, have failed to find intrinsic soil differences between hotspots and the surrounding matrix. Also, it remains unclear to what extent hotspots are associated with specific assemblages of nutrient‐rich plant species, as opposed to being a manifestation of intraspecific variation in nutritive quality. We conducted simultaneous studies in Kruger (South Africa) and Serengeti (Tanzania) National Parks to re‐evaluate the role of edaphic correlates of hotspot occurrence and to test whether intraspecific variation in plant quality occurs across hotspot‐matrix boundaries. We sampled soils and plants in paired hotspot and matrix plots at multiple sites within each ecosystem to test our a priori hypothesis that hotspots would be associated with distinct species assemblages and differences in soil fertility. We found clear hotspot‐matrix differences in foliar N, particularly within species, despite finding no differences in any soil or plant–soil variables, including N mineralization potential and mycorrhizal inoculation levels. We found only weak differences in community composition across the boundary, suggesting that intraspecific variation in foliar N rather than species turnover is mainly responsible for the enhanced nutritive value of hotspot vegetation. We propose that grazer–plant interactions may be stronger drivers of hotspot maintenance in these systems than plant–soil interactions.
Self-seeding winter cereal cover crops in soybean

Soil protection and nutrient scavenging benefits of cover crops have been widely reported. Nevertheless, adoption of cover crops in agronomic farming systems is low. Cover crop systems that do not require annual planting may increase adoption. The objectives of this study were to compare self-seeding and competitiveness of winter wheat (Triticum aestivum L.), triticale (x Triticosecale Wittmack), and rye (Secale cereale L.) using different planting configurations and management options while growing concurrently with soybean [Glycine max (L.) Merr. ]. Cover crops were planted with two or four 19-cm rows between each 76-cm soybean row. A no-cover crop check treatment was also included for comparison. Cover crop species and species x management system interactions were not significant for seed production or soybean seed yield. Averaged across management system, cereals produced 10 656 and 4051 seeds m -2 in 2004 and 2005. The two-row band, no-chop treatment (2RBNC) produced the most seed (20 347 and 14 511 seeds m -2 ) in 2004 and 2005, but also lowered soybean yield the greatest (45 and 40%). The four-row treatment with a late glyphosate band (4RLB) was the least competitive and yielded 3114 and 3717 kg ha -1 compared to 4019 and 4391 kg ha -1 in the check. Wheat had the greatest self-seeding, averaging about 31% of the original plant density. The four-row treatment without a glyphosate band (4RNB) could be used in organic production systems, although additional research is needed to develop less competitive self-seeding systems for conventional production systems.
AFM and Raman study of graphene deposited on silicon surfaces nanostructured by ion beam irradiation

Nanoscale structures were produced on silicon surfaces by low‐energy oxygen ion irradiation: periodic rippled or terraced patterns formed spontaneously, depending on the chosen combination of beam incidence angle and ion fluence. Atomic force microscopy image processing and analysis accurately described the obtained nanotopographies. Graphene monolayers grown by chemical vapour deposition were transferred onto the nanostructured silicon surfaces. The interfacial interaction between the textured surface and the deposited graphene governs the conformation of the thin carbon layer; the resulting different degree of regularity and conformality of the substrate‐induced graphene corrugations was studied and it was related to the distinctive topographical features of the silicon nanostructures. Raman spectroscopy revealed specific features of the strain caused by the alternating suspension and contact with the underlying nanostructures and the consequent modulation of the silicon–graphene interaction.
Cell Growth Stimulation, Cell Cycle Alternation, and Anti-Apoptosis Effects of Bovine Bone Collagen Hydrolysates Derived Peptides on MC3T3-E1 Cells Ex Vivo

Bovine bone collagen hydrolysates promote bone formation through regulating bone growth. However, the peptide sequences within these isolates have not been characterized. In this study, twenty-nine peptides from bovine bone collagen hydrolysates were purified and identified using nano-HPLC-MS-MS and Peak Studio analysis. HHGDQGAPGAVGPAGPRGPAGPSGPAGKDGR (Deamidation) and GPAGANGDRGEAGPAGPAGPAGPR (Deamidation) enhanced cell viability, inhibited apoptosis, and significantly altered the cell cycle of MC3T3-E1 osteoblast cells. These peptides were selected to perform molecular docking analysis to examine the mechanism underlying these bioactivities. Molecular docking analysis showed that these two peptides formed hydrophobic interactions and hydrogen bonds with epidermal growth factor receptor (EGFR) to activate the EGFR-signaling pathway, which may explain their bioactivity. These findings indicate that these and other similar peptides might be candidates for the treatment of osteoporosis.
Two Additions to the Turtle Fauna of Laos

Abstract Two geoemydid turtle species, Geoemyda spengleri and Cuora bourreti, are documented from Laos for the first time. The record of G. spengleri is based on photographs taken of a wild turtle by staff in a protected area in eastern Bolikhamxay Province, central Laos. Those of C. bourreti are based on our examinations of live turtles in the possession of a hunter and in a village in a remote area of eastern Savannakhet Province, southeastern Laos. Both localities lie near the border with Vietnam, where these species were previously known. Turtles are highly threatened in Laos from overexploitation for food and traditional medicine purposes, but the presence of G. spengleri and C. bourreti within protected areas offers hope for their persistence.
Identification and futuristic role of novel polymorphism of caprine PrP gene

Abstract The Caprine Prion Protein (PrP) gene polymorphism in three different native Indian goat populations of Southern Odisha, namely Ganjam (a registered breed of India), Ghumusari and Raighar was studied. The 876 bp amplified segment of PrP gene contains full length coding sequence of 771 bp. In Ganjam and Ghumusari goats, any difference of nucleotide sequence was not identified. However, the comparison of nucleotide sequences of Raighar goats and goats of other locality revealed a change in nucleotide at five different positions (G190A, G724A, A727T, C775G and C800T) which includes two non-synonymous nucleotide changes. The non-synonymous nucleotide change resulted a change in amino acid at two different positions (Ser234Cys and Lys246Phe) in mature polypeptide which were not reported earlier and therefore, considered as novel. On the basis of these variants of PrP gene phylogenetic tree was constructed which showed that Ganjam and Raighar goats appeared in different clade. Since any occurrence of Scrapie infection in goats of Odisha was not reported, it can be proposed that these changes in amino acid may be responsible as resistance allele.
Occurrence of Phyllostomus elongatus (Geoffroy St.-Hilaire, 1810) (Chiroptera, Phyllostomidae) in the Cerrado of Tocantins and a compilation of its Brazilian distribution

The lesser spear-nosed bat, Phyllostomus elongatus , is endemic of South America and in Brazil this species is recorded in Amazon, Atlantic Forest, Cerrado, and Pantanal. Here, we present a new record for P. elongatus in the savanna of central Brazil, known as the Cerrado. In January 2012, five individuals of P. elongatus were captured and recorded in a limestone cave in the Aurora do Tocantins county, Tocantins State. Phyllostomus elongatus has already been registered in 32 locations and 14 Brazilian states, and their records appear to be associated with humid habitats and forested areas.
A Model of Feeding by Parasitic Lampreys

We derived a quantitative feeding model to estimate energy intake by parasitic sea lampreys (Petromyzon marinus) as a function of lamprey mass, host mass, and attachment time. Comparison of model predictions with observed growth by lampreys with known feeding histories suggests that the feeding model, used in conjunction with a previous model of lamprey energetics, generates unbiased predictions of energy intake and subsequent growth. On the basis of the relationship between energy intake and attachment time, and in accordance with previous theory on partial prey consumption, we hypothesized that duration of attachment by lampreys to individual hosts should vary inversely with host density. No significant difference in attachment time or latency to attack at two host densities could be detected, although the first attachment by a lamprey tended to be longer than its second, regardless of host density.
Reliability and validity of the Turkish version of the Vocal Fatigue Index1 This study was given as an oral presentation at the 41th Turkish National Otorhinolaryngology and Head Neck Surgery Congress,Antalya, 2019.

Background/aim The aim of this study is to evaluate the reliability and validity of the Turkish version of the Vocal Fatigue Index (VFI). Materials and methods The study was conducted with 535 participants including 285 patients with voice disorders and 250 healthy controls. Internal consistency and test-retest reliability were calculated for the reliability analysis. The mean VFI factor scores of both groups were compared. The strength and direction of the relation between VFI and Voice-Related Quality of Life (V-RQOL) measure was evaluated for the validity analysis. Results The Cronbach’s alpha coefficient of VFI factor scores was found to be 0.920 for tiredness and avoidance of voice use, 0.879 for physical discomfort with voice use, and 0.882 for improvement of symptoms with voice rest. The test-retest reliability revealed 0.877 for the tiredness and avoidance of voice use, 0.913 for the physical discomfort with voice use, and 0.820 for the improvement of symptoms with voice rest. When compared with healthy individuals, VFI factor scores were statistically significant higher in patients with voice disorders. The V-RQOL scores decreased significantly as the VFI scores increased. Conclusion The Turkish version of the VFI is a good reliable and valid instrument for evaluating vocal fatigue symptoms in the Turkish-speaking community.
MORPHOLOGY OF THE DIATOM GENUS CAMPYLONEIS (BACILLARIOPHYCEAE, BACILLARIOPHYTA), WITH A DESCRIPTION OF CAMPYLONEIS JULIAE SP. NOV. AND AN EVALUATION OF THE FUNCTION OF THE VALVOCOPULAE 1

A revision of the monoraphid pennate diatom genus Campyloneis Grunow was carried out based on LM and EM observations. The material examined originated from various herbarium collections and from extant epiphytic diatom communities on leaves of Posidonia spp. We also examined the generitype C. grevillei (Smith) Grunow and the fossil material of C. gheyselinchi Reinhold from which the author extracted the type. Our results clarified the fine structure of C. grevillei and C. gheyselinchi. Of the various varieties of C. grevillei, only the variety argus (Grunow) Cleve was retained. This differs from the nominate variety in the arrangement and shape of the areolae adjacent to the sternum of the araphid valve. The newly described taxon Campyloneis juliae De Stefano differs from all Campyloneis species in areolae ultrastructure and morphology of the valvocopulae. As for the fossil species C. gheyselinchi, the sternum valve areolae are similar to those of C. grevillei, but scarcity of frustules in the type material prohibited evaluation of its variability. For this reason we provisionally maintained its rank of species. The elaborate linking systems among the valvocopulae and valves in Campyloneis species appear to provide structural reinforcement against pressure from neighboring epiphytic diatoms and scouring of seagrass leaves.
Effect of Precipitation and Temperature on Larval Survival of Cephus cinctus (Hymenoptera: Cephidae) in Barley Cultivars

Abstract Host plant traits strongly affect survivorship of insect herbivores, and host suitability is especially important for the wheat stem sawfly, Cephus cinctus Norton, which spends its entire egg, larval, and pupal periods in a single stem. Measuring larval survival inside stems from egg hatch through diapause-mediated dormancy is a potential measure of population size for the next year but is also useful in assessing effects of growing season precipitation and temperature. Larval growth is synchronized with host plant growth, and the larva cannot switch hosts. Thus, incorporating plant physiological time, as growing degree days (GDD), may yield a better prediction of larval survival. Therefore, we assessed wheat stem sawfly survival from early larval growth to the beginning of autumnal diapause in barley cultivars selected from across feed, forage, and two- or six-row malt groups. Field experiments were conducted in Gallatin and Chouteau counties, Montana, in 2016 and 2017. We used Kaplan-Meier estimation to assess larval survival among cultivars. We found that the survival of pre-diapause larvae was greatest in ‘Hockett' (36.5%) and lowest in ‘Celebration’ (15.4%). Precipitation and temperature during the growing season affected temporal patterns for larval survival across study sites. Adjusting survivorship curves using site-specific GDD accumulation allowed cultivar-specific survivorship to be estimated more precisely for each site, despite differing environmental influences. Our findings suggest that measuring wheat stem sawfly survival across barley cultivars and standardizing by site-specific GDDs may provide better recommendations on barley cultivars that impede wheat stem sawfly population growth and reduce economic losses.