Miracle-dz/UniFAR-FTUs huggingface dataset:
High Prevalence of Superior Labral Anterior-Posterior Tears Associated With Acute Acromioclavicular Joint Separation of All Injury Grades

Background: Despite the relatively high number of cases of acromioclavicular joint (AC) separation in the athletic population, optimal clinical outcomes are not achieved in every case. Limited data exist regarding the prevalence of intra-articular glenohumeral pathologies (IAPs) associated with acute AC separation of all injury grades. Purpose: To determine the prevalence of IAPs associated with AC separation, regardless of severity. Study Design: Case series; Level of evidence, 4. Methods: A total of 62 patients (mean age, 37.6 years) with acute AC separation were included in this study; 41 were nonoverhead recreational athletes. All patients underwent magnetic resonance arthrography (MRA) to evaluate for IAPs. Arthroscopic data from patients undergoing surgical treatment were correlated with MRA results. Results: Patients sustained acute AC separation of Rockwood grade 1 (16.1%), grade 2 (46.8%), grade 3 (25.8%), and grade 4 (11.3%). A concomitant IAP was present in 48 of 62 (77.4%) patients and included superior labral anterior-posterior tears (72.6%), anterior labral tears (24.2%), posterior labral tears (4.8%), supraspinatus tears (3.2%), and inferior glenohumeral ligament ruptures (1.6%). There were 18 (29.0%) patients who had a concomitant pathology in >1 intra-articular structure (combined IAPs). Additionally, 71.8% of patients with grade 1 and 2 AC separation had associated IAPs, and 23.1% had combined IAPs. Furthermore, in patients younger than 40 years, 64.0% of those with grade 1 to 3 AC separation demonstrated associated labral pathologies. There was no difference when comparing age or severity of AC separation and the prevalence of concomitant labral tears (P = .36 and .22, respectively). Conclusion: There was a high prevalence of IAPs among patients undergoing MRA after AC separation. While an IAP has been described in association with high-grade AC separation previously, the high prevalence of IAPs in low-grade separation in our study was unexpected and suggests that a thorough evaluation and clinical follow-up for patients with all grades of AC separation may be beneficial.
Purification of Organelles from Mammalian Cells

The protocols in this unit illustrate a range of different procedures that have been used to fractionate tissue homogenates. They emphasize different fractionation techniques that have been used for rat liver, an abundant tissue that has been a favorite of many investigators and has served as the source of many organelle preparations of excellent purity. For selected procedures, other examples have been given using other tissue sources (e.g., glandular tissues that maintain protein storage granules for regulated secretion) or, where particularly favorable, cultured cells. The basis (or goal) of each separation and the merits and limitations of each procedure are summarized to provide a guide for selecting among the various approaches. The large number of protocols include specific details relevant to a particular sample cell type (and in many cases a particular organelle).
MOLECULAR FINGERPRINTING OF RECENTLY NOTIFIED SUGARCANE (SACCHARUM L.) VARIETIES USING STMS MARKERS

DNA fingerprints of 13 recently notified sugarcane varieties for commercial cultivation for Peninsular zone (Co 99004, Co 2001-13, Co 2001-15, Co 0218, Co 0403 and Co 06027), North Western zone (Co 0118, Co 0237, Co 0238, Co 0239, Co 05009 and Co 05011) and East coast zone (Co 06030) have been developed to aid their unambiguous identification using a set of sugarcane specific sequence tagged microsatellite markers. Among the primers, NKS 23 produced more number of unique bands in the investigated material. Based on the bands detected on silver stained 7.5% non-denaturing polyacrylamide gels that resolved the PCR products, unique bands specific to each variety were identified. This information along with the overall banding profile would serve as fingerprints of each variety for proper varietal identification in the context of plant variety protection and varietal registration. As sugarcane is vegetatively propagated, these fingerprints remain uniform and stable making fingerprinting a reliable method of varietal identification in the crop. Moreover, genetic diversity among the clones was quantified through graphical genotyping using GGT software that revealed a moderate genetic similarity of 0.773 among the varieties which are gene pools for high yield, juice quality and resistance to various abiotic and biotic stresses. Three genetically more diverse clones (Co 06027, Co 06030 and Co 05011) and 22 diverse combinations have also been identified for their judicious utilization in breeding for better genetic gains.
Association of ADRB2 rs1042713 with Obesity and Obesity-Related Phenotypes and Its Interaction with Dietary Fat in Modulating Glycaemic Indices in Malaysian Adults

Gene-diet interaction studies have reported that individual variations in phenotypic traits may be due to variations in individual diet. Our study aimed to evaluate (i) the association of ADRB2 rs1042713 with obesity and obesity-related metabolic parameters and (ii) the effect of dietary nutrients on these associations in Malaysian adults. ADRB2 genotyping, dietary, physical activity, anthropometric, and biochemical data were collected from 79 obese and 99 nonobese individuals. Logistic regression revealed no association between ADRB2 rs1042713 and obesity (p=0.725). However, the carriers of G allele (AG + GG genotypes) of rs1042713 were associated with increased odds of insulin resistance, 2.83 (CI = 1.04–7.70, adjusted p=0.042), in the dominant model, even after adjusting for potential confounders. Obese individuals carrying the G allele were associated with higher total cholesterol (p=0.011), LDL cholesterol levels (p=0.008), and total cholesterol/HDL cholesterol ratio (p=0.048), compared to the noncarriers (AA), even after adjusting for potential confounders. Irrespective of obesity, the carriers of GG genotype had significantly lower fasting glucose levels with low saturated fatty acid intake (<7.3% of TE/day) (4.92 ± 0.1 mmol/L vs 5.80 ± 0.3 mmol/L, p=0.011) and high intake of polyunsaturated fatty acid:saturated fatty acid ratio (≥0.8/day) (4.83 ± 0.1 mmol/L vs 5.93 ± 0.4 mmol/L, p=0.006). Moreover, the carriers of GG genotype with high polyunsaturated fatty acid intake (≥6% of TE/day) had significantly lower HOMA-IR (1.5 ± 0.3 vs 3.0 ± 0.7, p=0.026) and fasting insulin levels (6.8 ± 1.6 µU/mL vs 11.4 ± 2.1 µU/mL, p=0.036). These effects were not found in the noncarriers (AA). In conclusion, G allele carriers of ADRB2 rs1042713 were associated with increased odds of insulin resistance. Obese individuals carrying G allele were compromised with higher blood lipid levels. Although it is premature to report gene-diet interaction on the regulation of glucose and insulin levels in Malaysians, we suggest that higher quantity of PUFA-rich food sources in regular diet may benefit overweight and obese Malaysian adults metabolically. Large-scale studies are required to replicate and confirm the current findings in the Malaysian population.
Prevalência de anticorpos anti-Toxoplasma gondii e anti-Neospora caninum em rebanhos caprinos do município de Mossoró, Rio Grande do Norte

A toxoplasmose e uma doenca que acomete todos os animais endotermicos, inclusive o homem. Nos caprinos pode causar transtornos reprodutivos, gerando grandes perdas economicas. O Neospora caninum foi recentemente reconhecido e, apesar de causar problemas reprodutivos em caprinos, ainda sao poucos os trabalhos realizados nesta especie. Com o objetivo de verificar a soroprevalencia destes agentes em caprinos do municipio de Mossoro, Rio Grande do Norte, amostras de soro de 381 animais (324 femeas e 57 machos) de 14 propriedades foram testadas pela Reacao de Imunofluorescencia Indireta a partir das diluicoes 1:64 e 1:50 para Toxoplasma gondii e N. caninum, respectivamente. Das 14 propriedades, 13 (92,8%) apresentaram animais soropositivos para T. gondii e quatro (28,6%), para N. caninum. Dos 381 animais amostrados, 65 estavam positivos para T. gondii (17,1%) e quatro (1,05%) para N. caninum. Nao houve associacao estatistica entre a soropositividade aos agentes e o sexo, a presenca de problemas reprodutivos e a presenca de caes e/ou gatos nas propriedades. Os resultados indicaram uma baixa soroprevalencia ao N. caninum no municipio, enquanto T. gondii encontra-se disseminado nos rebanhos caprinos da regiao.
Remote protein homology as a spyglass to the past

Contemporary proteins evolved by the acquisition, recombination, and adaptation of established building blocks called domains. Most domains already existed at the time of the last universal common ancestor and then diverged, leaving weak signatures of their homology, i. e. common ancestry. Yet, the rapid growth of protein databases and improved algorithms revealed distant homologies of domains hitherto deemed unrelated. Besides evolutionary implications, these findings also enable the transfer of knowledge between similar proteins. It is important to probe the strengths, weaknesses, and limits of these methods to leverage this progress. To this end, we analyzed remote homologs in bioinformatic case studies. First, we analyzed the uncharacterized SMP domain abundant in the ERMES complex, which tethers the endoplasmic reticulum to mitochondria and positively impacts inter-membrane phospholipid transfer. We established the BPIand Takeout-like families as SMP domain homologs. As both families comprise hydrophobic ligand binders and share a fold, we predicted the same fold and an active role in phospholipid transfer for SMP domains. Finally, we grouped the three families in the novel tubular lipid-binding proteins (TULIP) superfamily. Next, we searched for different folds with homology to the repetitive subunit of β-propellers, the blade, and initially detected four candidates. Further evaluation confirmed blade homologs in type II βprism and IRE1-LD proteins, but revealed that WW domains and βpinwheels have arisen convergently. These findings stress the importance of fold-spanning relationships for classification systems. Lastly, we analyzed the tetratrico peptide repeat (TPR) motif to probe the lower sequence length limit in homology detection. We were unable to expand on known TPR homologs and our data did not allow us to infer an evolutionary scenario for TPR-like motifs. Due to a discussed origin from single motif instances, we also searched for TPR domains recently amplified from non-repetitive singleton instances but were unable to detect any and thus believe that this process is not ongoing. Overall, our results help to determine more clearly the uses and limits of remote homology detection algorithms. Blade-sized fragments are within reach of current methods, whereas TPRs are already borderline cases. Further, the remote homologies uncovered in this work contribute to a growing knowledge base on protein evolution, which will eventually lead to a protein classification by natural descent.
Characterization of diversified cytoplasmic genetic male sterile (A) and restorer (R) lines of pigeonpea for good heterotic combinations

The study encompassed characterization of 45 newly identified stable CGMS (A) and 26 restorer (R) lines of different genetic backgrounds grown in augmented design during kharif 2008. All the A and R lines exhibited enormous phenotypic variability. ‘CMS GT 731’ (142 days), ‘CMS GT 723’ (143 days) and ‘CMS GT 721’ (144 days) among A lines and ‘GTR 71’ (143 days) among R lines were the earliest in maturity. ‘CMS GT 726’, ‘CMS GT 731’, ‘CMS GT 701’, ‘CMS GT 721’, ‘CMS GT 725’, ‘CMS GT 729’, ‘CMS GT 737’ and ‘CMS GT 738’ among A lines and ‘GTR 71’, ‘GTR 74’, ‘GTR 66’ and ‘GTR 68’ among R lines evinced early flowering lines having good nicking. On account of having different seed colour, seed size and growth habit, the newly identified lines were grouped according to maturity, growth habit, seed size and seed colour making it feasible to select good nicking A and R lines to develop situation specific hybrids as per consumers’ preference.
Análise do genoma completo de um isolado de Sapovirus no Distrito Federal e expressão do capsídeo do vírus para a produção de "Virus-like particles" pelo sistema de baculovírus recombinantes

The family Caliciviridae consists of viruses belonging to five genera: Sapovirus, Norovirus, Lagovirus, Vesivirus and Nebovirus. Certain sapovirus and norovirus strains are well-known causative agents of serious human gastroenteritis. Sapovirus is the second most important causative agent of human diseases next to norovirus. The sapovirus genome is linear, positive-sense, single-stranded RNA, of approximately 7,5kb that is polyadenylated at the 3’ terminus. Sapovirus is divided into, at moment, seven genogroups (GI-GVII). This classification is based mainly on capsid protein sequence divergence. In this study, the entire genome of one sapovirus isolated in Brasilia, Brazil (Sapovirus Hu/GI.2/BRDF01/BRA/2009) was evaluated with all available sequences of sapovirus to determine its phylogenetic relationship and possible intraand inter-genogroups recombination events using RDP3 program. It was determined the identity between the Brazilian sequence and one sequence collected in 2005 in Bangladesh and its possible recombination such as a possibility of an inter-genogroup recombination event between GI (human) and GIII (porcine). Another relevant found is the region of RdRp-CP as a hot spot of recombination. Due to the lack of the efficient diagnostic tools based on ELISA procedure, the preparation of capsid protein of the virus using heterologous protein expression system was requested. Thus the second objective of this work was to produce VLP sapovirus using recombinant baculovirus system. To confirm this particle assembly besides electronic microscopy analysis a polyclonal antibody was produced against the variable region (P2) of the capsid protein. The analysis by transmission electron microscope showed spherical particles with sizes of 20-40 nm, however the response between the anti-P2 and the possible VLP could not be demonstrated. These results indicate that further studies regarding the expression and purification of VLP sapovirus should be performed. Key-words: calicivirus, sapovirus, recombination, production of policlonal antibodies, virus-
Proliferative and nutritional dependent regulation of glyceraldehyde‐3‐phosphate dehydrogenase expression in the rat liver

Abstract. Glyceraldehyde‐3‐phosphate dehydrogenase is a multifunctional protein possessing numerous cytoplasmic and nuclear functions associated with cellular proliferation. Despite the emerging role of glyceraldehyde‐3‐phosphate dehydrogenase in regulating the proliferative process, there is a paucity of data regarding its expression and intracellular distribution in non‐malignant proliferating hepatocytes. Thus the aim of the present study was to document the intracellular distribution of glyceraldehyde‐3‐phosphate dehydrogenase protein in proliferating hepatocytes derived from regenerating rat livers, and glyceraldehyde‐3‐phosphate dehydrogenase gene expression in fasted and re‐fed rats following partial hepatectomy (PHx). Glyceraldehyde‐3‐phosphate dehydrogenase mRNA and protein expression were documented by Northern and Western blot analyses, respectively, at various times following 70% PHx in adult Sprague–Dawley rats. At 24 h post‐surgery, glyceraldehyde‐3‐phosphate dehydrogenase mRNA expression was significantly increased in both PHx and sham operated rats (P < 0.001), respectively. Despite the increase in glyceraldehyde‐3‐phosphate dehydrogenase mRNA expression in both groups, only PHx rats had a significant increase in the nuclear fraction of glyceraldehyde‐3‐phosphate dehydrogenase protein (threefold increase compared to sham and baseline levels, P < 0.01), cytoplasmic levels of glyceraldehyde‐3‐phosphate dehydrogenase protein remained unaltered in both groups. In terms of the effects of feeding and fasting on rats there were no significant differences in glyceraldehyde‐3‐phosphate dehydrogenase mRNA levels, whether fasted or refed, in rats that had undergone PHx, 8 h earlier. On the other hand, glyceraldehyde‐3‐phosphate dehydrogenase mRNA levels were significantly increased in refed compared to fasted sham operated rats 8 h following surgery. Serum insulin concentrations were higher in the refed PHx and sham groups compared to their fasted counterparts. The results of this study indicate that although glyceraldehyde‐3‐phosphate dehydrogenase mRNA are altered to the same extent in PHx and sham‐operated rats following surgery, increases in the nuclear fraction of glyceraldehyde‐3‐phosphate dehydrogenase protein only occur in PHx rats. The results also indicate that glyceraldehyde‐3‐phosphate dehydrogenase expression is affected by the nutritional status of animals undergoing abdominal sham surgery.
Identification and Molecular Characterization of Z/ZE Lineage MHC Class I Heavy Chain Homologue and β2-microglobulin from Rock Bream Oplegnathus fasciatus

We identified and characterized ful-length cDNAs of rock bream Oplegnathus fasciatus major histocompatibility complex (RbMHC) class I and b 2-microglobulin (Rbb 2m) molecules. The fullength RbMHC class I cDNA was 2,667 bp with a 1,227 bp open reading frame encoding 409 amino acids (aa). The Rbb 2m ful-length cDNA (1,339 bp) consisted of a 354 bp coding region, encoding 118 aa. RbMHC class Ia was clustered with the Z/ZE lineage of known MHC class I sequences, suggesting a novel molecule belonging to the Z/ZE lineage. Although characteristic features (residues and motifs) known to be conserved in classical and non-classical class I molecules were conserved in RbMHC class Ia with few modifications, it is more closely resembled to classical MHC class I. RbMHC class I and Rbb 2m were transcribed constitutively in healthy fish, but expression difered among the diferent organs and was highest in whole blood. Low sequence variation in the RbMHC class I a 1 region makes it uncertain whether the molecule belongs to the non-classical group. However, because transcription was induced by megalocytivirus, the molecule is most likely a member of the classical group. Our results provide important information for future studies on antigen presentation and cytotoxic CD8 T cel responses in rock bream against infectious pathogens.
Spatio‐temporal dynamics of a tree‐killing beetle and its predator

&NA; Resolving linkages between local‐scale processes and regional‐scale patterns in abundance of interacting species is important for understanding long‐term population stability across spatial scales. Landscape patterning in consumer population dynamics may be largely the result of interactions between consumers and their predators, or driven by spatial variation in basal resources. Empirical testing of these alternatives has been limited by the lack of suitable data. In this study, we analyzed an extensive network of spatially replicated time series to characterize the local and regional processes affecting spatio‐temporal dynamics of a tree‐killing bark beetle (Dendroctonus frontalis or SPB) and its key predator (Thanasimus dubius) across the southeastern United States. We first used a mechanistic model to evaluate factors affecting the stability of 95 predator–prey time series and then conducted spatial analyses to evaluate scale dependence in the factors affecting the geographical patterning of this system. Across the region, population fluctuations of both species were correlated in space beyond 400 km but there was notable spatial variation in the deterministic and stochastic processes influencing forest‐scale (local) fluctuations. Time series analyses indicated that local dynamics of SPB and T. dubius are not cyclical. Instead, the abundance of T. dubius responded almost instantaneously to changes in SPB abundance. Spatial variation in long‐term forest‐scale abundance of both species was linked most strongly to the abundance of pine habitat indicating a stronger role for resource availability in SPB population dynamics than top‐down effects. Our results are consistent with other studies indicating that animal populations tend to be synchronized in space via spatially correlated processes such as weather; yet local dynamics tend to be linked to smaller‐scale host patterns. Our study provides a rare empirical assessment of how local processes scale up to produce landscape patterns that influence forest ecology and forest management.
Rooting from callus of Jatropha cuneata (Wiggins & Rollins) in vitro

The genus Jatropha is important for its medicinal properties and it is thought that could become a source of oil with the potential to displace in the future the sources of conventional fuels. In the state of Sonora there are several species of Jatropha, one of them is Jatropha cuneata, which needs to be studied because it is a species with great economic potential, as it represents a possible alternative for sustainable energy development of biodiesel. Taking advantage of the in vitro culture studies are being done with the plant Jatropha cuneata. Leaves were used from the plant were disinfected and planted aseptically in MS medium containing the growth regulator ANA (0, 1, 1.5 and 2 mGL-1) combined with 0, 0.5 and 1 mGL-1 kinetin, obtaining the highest calluses formation with 1 mgL-1 of both regulators of growth. The obtained callus, were subcultured in culture medium containing combinations of ANA with kinetin: ANA at concentrations of 0, 1, 1.5 and 2 mGL-1 and kinetin in concentrations of 0, 0.5 , 1, 1.5 and 2 mGL-1 getting rooting in the calluses that had been subjected in culture media containing concentrations of 1 and 1.5 mGL-1 of ANA. Also callus were subcultured in 0, 1, 1.5 , 2 and 2.5 mGl-1 of 2, 4-D, 0, 1, 1.5 , 2, and 2.5 mGl-1 of the growth regulator kinetin, showing no significant differences in the calluses subject at 1, 1.5 and 2 mGl-1 of 2, 4-D and kinetin.
Short-term Spectral Slope Measures and their Sensitivity to Speaker, Vowel Identity and Prominence Ukazatele krátkodobého spektrálního sklonu a jejich citlivost na mluvčího, identitu vokálu a prominenci

This study examines ten methods of measuring short-term spectral slope with the primary aim of quantifying vowel prominence. A highly controlled dataset consisting of 45 pseudowords with varied placement of prominent vowel read by 12 speakers was used. The investigated methods included Hammarberg index, α-measure, linear regression, differences of spectral energies in separate frequency bands, difference between amplitudes of the first two formants and spectral emphasis. All of the methods showed substantial sensitivity to speaker and vowel identity in particular. Nevertheless, most of the methods were also able to discriminate among prominent and non-prominent realizations of the vowels. The difference between sums of energy in two adjacent frequency bands separated by a floating pivot locked to the value of the second formant proved to be the most successful measure. On the contrary, linear regression of the spectrum performed worst. Also, exclusion of the fundamental frequency band decreased performance of the methods significantly. The vowel /i/ was shown to be the most sensitive to prominence, whereas /u/ appeared to be the least useful for quantifying both prominence and speaker identity. A considerable speaker discrimination potential of the methods was also corroborated.
Identification of Protein Interactions

P rotein interactions are intrinsic and vital to many cellular processes. In recent years many new techniques have been developed for the study of this important topic; the review by Phizicky and Fields (1995) provides an excellent general overview of this subject. This chapter describes biochemical, physical, and genetic methods that are used to detect specific protein interactions. The companion Chapter 20 presents a series of complementary methods that are used to provide quantitative information about protein interactions, such as the strength and kinetics of binding.