Miracle-dz/UniFAR-FTUs huggingface dataset:
Models of the Primary and Secondary Structure for the 12S rRNA of Birds: A Guideline for Sequence Alignment

Models of the primary and secondary structure for the 12S ribosomal RNA (rRNA) gene of birds is presented based on a comparison of 100 species. Preliminary higher-order structures were delimited following the model for vertebrates. Paired regions were refined following a complementary base-pairing criterion and compensatory mutations were considered as a further confirmation of their existence. The model shows 40 stems, 20 internal loops and 17 external loops, arranged in the typical four domains suggested for the small subunit rRNA. The higher-order structures recovered in the model were used to build a multiple sequence alignment appropriate for phylogenetic analysis. The phylogeny recovered from this alignment was compared with trees inferred from alignments assembled using different alignment parameters in the program ClustalW. The alignment based on the secondary structure is sensitive to positional covariation of stems. Nonetheless, the phylogeny recovered with this method resulted in relationships that are more congruent with non-molecular data than those inferred from alternative alignments.
The influence of preoperative MRI in early breast cancer: gold standard.

BACKGROUND Aim of this study was to evaluate the impact of presurgical breast MRI on the surgical management of selected patients with early-stage breast cancer, who were candidates for BCT. MATERIALS AND METHODS The trial was built up according to the major European Breast Society. In additional foci classified as BI-RADS 3-4 (4a, 4b, and 4c), a targeted second-look US study was performed. RESULTS A total of 123 patients underwent presurgical breast MRI. Therapeutic strategy established based on MRI was appropriate in 83.8% of cases. Analysis carried out on the subgroup of patients with dense breast showed that additional foci were found in 41.9% and a greater local extension of the index lesion in 6.4%. CONCLUSION The results obtained in the subgroup of patients with high breast density suggest the importance of a sensitive tool such as MRI in the local staging of breast cancer before treatment planning. KEY WORDS Breast cancer, BI-RADS, Histological diagnosis, Mammography MRI.
Effects of temperature and elevated CO2 on cell division in shoot meristems: differential responses of two natural populations of Dactylis glomerata L.

The aim was to establish whether temperature and/or elevated [CO2] (-700 μmol mol−1) affects the cell doubling time (cdt) in the different zones of the shoot apex of two natural populations of Dactylis glomerata originating in Portugal (38° S3′ N) and in Sweden (63° 09′ N). In the Portuguese population at ambient [CO2], only the pith rib meristem (PRM) exhibited a significant shortening of cdts from 10 to 30 °C. Elevated [CO2] resulted in a significant shortening of cdt, particularly in the PRM where cdt was reduced 4-8- and 6-1-fold at 10 and 20 °C, respectively, but only 2-fold at 30 °C. In the Swedish population at ambient [CO2], there were no consistent temperature-dependent alterations to cdt and this population was less responsive to elevated [CO2] than the Portuguese population. Nevertheless, elevated [CO2] resulted in a significant shortening of the cdt for some of the zones; the maximum reduction occurred in the PRM at 30 °C. We concluded that in the shoot apex of the Portuguese population, and most notably in the PRM, 10 and 20 °C were non-optimal temperatures for cell division, whilst the Swedish population was relatively buffered against temperature change. Elevated [CO2] resulted in substantially greater reductions in cdts in the shoot meristem of the Portuguese population than in that of the Swedish population.
Bioinformatics profiling integrating a four immune-related long non-coding RNAs signature as a prognostic model for papillary renal cell carcinoma

Background: Papillary renal cell carcinoma (pRCC) was the 2nd most common subtype, accounting for approximately 15% incidence of renal cell carcinoma (RCC). Immune related long non-coding RNAs (IR-lncRs) plentiful in immune cells and immune microenvironment (IME) are potential in evaluating prognosis and assessing the effects of immunotherapy. A completed and meaningful IR-lncRs analysis based on abundant pRCC gene samples from The Cancer Genome Atlas (TCGA) will provide insight in this field. Results: 17 IR-lncRs were selected by Pearson correlation analysis of immune score and the lncRNA expression level, and 5 sIRlncRs were significantly correlated with the OS of pRCC patients. 4 sIRlncRs (AP001267.3, AC026471.3, SNHG16 and ADAMTS9-AS1) with the most remarkable prognostic values were identified to establish the IRRS model and the OS of the low-risk group was longer than that in the high-risk group. The IRRS was certified as an independent prognosis factor and correlated with the OS. The high-risk group and low-risk group showed significantly different distributions and immune status through PCA and GSEA. In addition, we further found the expression levels of SNHG16 was remarkably enhanced in female patients with more advanced T-stages, but ADAMTS9-AS1 showed the opposite results. Conclusion: The IRRS model based on the identified 4 sIRlncRs showed the significant values on forecasting prognoses of pRCC patients, with the longer OS in the low-risk group. Methods: We integrated the expression profiles of LncRNA and overall survival (OS) in the 322 pRCC patients based on the TCGA dataset. The immune scores calculated on account of the expression level of immune-related genes were used to verify the most relevant IR-lncRs. Survival-related IR-lncRs (sIRlncRs) were estimated by COX regression analysis in pRCC patients. The high-risk group and low-risk group were identified by the median immune-related risk score (IRRS) model established by the screened sIRlncRs. Functional annotation was displayed by gene set enrichment analysis (GSEA) and principal component analysis (PCA), and the immune composition and purity of the tumor were evaluated through microenvironment cell count records. The expression levels of sIRlncRs of pRCC samples were verified by real-time quantitative PCR.
L-carnitine and its functional effects in poultry nutrition

L-carnitine has indispensable functions in intermediary metabolism and is received by endogenous synthesis and from exogenous sources. It plays an obligate role in fatty acid metabolism by directing fatty acids into the mitochondrial oxidative pathway through the action of specialised acyltransferases. In poultry production, L-carnitine has a multi functional purpose, which includes: growth promotion, strengthening the immune system, antioxidant effects and improving semen quality. The concentration of L-carnitine in animals varies widely across species, tissue type, and nutritional status of the animal. It has been suggested that the L-carnitine requirement may be increased under certain circumstances such as via higher performance, various stress conditions and where the diet is deficient in animal protein sources. The review of L-carnitine functions uniquely includes the main aspects of this consequential feed supplementary inclusion in poultry nutrition.
Regulation of metabolic shifts in Clostridium acetobutylicum ATCC 824

Abstract Alcohol formation was initiated in continuous cultures of Clostridium acetobutylicum under distinct steady-state conditions: (i) in glucose-limited cultures established at low operating pH with formation of butanol, ethanol and acetone (induction of the solventogenesis) in which cells contained normal levels of NADH and a high level of ATP and butyric acid; and (ii) by increasing the NADH pressure at neutral pH in glucose-limited cultures after addition of Neutral red, or in glucose-glycerol or glucose-glycerol-pyruvate grown cultures, with a strictly alcohologenic metabolism (no acetone produced) associated with high levels of intracellular NADH and various levels of ATP. These two different metabolic shift systems are correlated with the expression of different genes involved in the solvent-forming pathways and the electron flow distribution. A high NADH level leading to butanol and ethanol formation was accompanied by increased activities of the NADH-dependent alcohol and butyraldehyde dehydrogenases, and ferredoxin:NAD(P) + reductases, and by decreased activities of the NADH:ferredoxin reductase. This last group of enzymes constitutes the key enzymes regulating electron flow, since no change in hydrogenase activity was observed. On the other hand, classical solventogenesis appears to be characterized by high levels of expression of the NADPH-dependent alcohol and butyraldehyde dehydrogenases, and of the two enzymes involved in the acetone-forming pathway, while the ferredoxin:NAD(P) + reductases were not synthesized. A decrease of the in vitro hydrogenase activity explains the lower hydrogen generation. In addition, the regulation of the intracellular pH was different between the alcohologenic culture grown at neutral pH and the solventogenic cultures grown at low pH. An inversion of the transmembrane pH gradient was observed during the production of alcohol at neutral pH and was related to a lower in vivo specific rate of hydrogen production while in the cultures grown at low pH the transmembrane pH generation was not linked to the F 1 F 0 ATPase activity.
Candidate regions for a testicular cancer susceptibility gene

Epidemiological data suggest the presence of a susceptibility gene for testicular cancer in some families. Families with multiple cases of testicular cancer are rare and almost all those reported have only two affected members. We have performed a sib-pair analysis on 35 families in which there are either two or three affected brothers. These families have been typed for 220 autosomal microsatellite markers spaced 10-20 cM throughout the genome. Six regions which gave a LOD score of more than 1.0 on formal linkage analysis or a P value of 0.05 or less using a non-parametric approach are considered as candidate regions for a susceptibility gene. Of particular interest is one region on chromosome 4. Two neighbouring probes in this region both scored positively with LOD score of 2.60 on multipoint analysis. An International Testis Cancer Linkage Consortium has been formed to pool resources and will investigate these findings further with the world-wide collection of families.
Chemotaxonomic clarification of pharmaceutically important species of Cyperus L.

The evaluation of the crude herbal drug which eventually enters the pharmaceutical market is obviously of considerable importance. This operation involves the identification of the material and determination of its quality, purity and of adulterated nature of the adulterants. The present paper is based on the above objectives which confined to chemotaxonomic authentication of Cyprus rotundus L. (Nagar mootha) and its other similar species. Chemotaxonomic techniques including morphology, organoleptography, palynology, anatomy and phyto-chemical analysis were carried out in order to clarify the pharmaceutically important species of Cyperus that is Cyperus rotundus, Cyperusalopecuroides, Cyperus difformis and Cyperus niveus. It is concluded from this study that the genuine source of herbal drug Nagar Mootha is C. rotundus instead of other species. Such type of studies is the need of herbal industry to ensure validation process which applied in the manufacturing of herbal medicines and phyto- pharmaceuticals. This will provide the credibility in the regulation and grown of pharmaceutically important herbal medicines for the foreseeable. Key words: Cyperus L. , chemotaxonomic, pharmaceutical.
The development of a Chinese Healthy Eating Index for School-age Children and its Application in children from China Health and Nutrition Survey

Abstract This study aimed to develop a Chinese Healthy Eating Index for School-age Children (CHEI-SC), apply it in the 2011 China Health and Nutrition Survey (CHNS) to assess dietary quality, and compared it with our former developed index named CHEI. Data of 3-day 24-hour diet recalls and household food inventory survey from 1600 school-age children in CHNS-2011 were used to develop the CHEI-SC, using the methods of standard portion size, energy-density-based approach, and least restrictive approach. The CHEI-SC included 19 components with a total score (T-score) ranging from 0 to 100. The investigated children had a median score of 49.6. Children with a higher T-score were more likely to have higher social economic status (SES), higher level of urbanisation, fewer family size, and regularly attending school. The CHEI-SC was able to assess dietary quality of Chinese school-age children, was sensitive to demographics, and more comprehensive and accurate than the CHEI. Graphical Abstract
Does surgical procedure type impact postoperative pain and recovery in deep inferior epigastric artery perforator flap breast reconstruction?

Background The deep inferior epigastric artery perforator (DIEP) flap is the commonest flap used for breast reconstruction after mastectomy. It is performed as a unilateral (based on one [unipedicled] or two [bipedicled] vascular pedicles) or bilateral procedure following unilateral or bilateral mastectomies. No previous studies have comprehensively analyzed analgesia requirements and hospital stay of these three forms of surgical reconstruction. Methods A 7-year retrospective cohort study (2008–2015) of a single-surgeon’s DIEP-patients was conducted. Patient-reported pain scores, patient-controlled morphine requirements and recovery times were compared using non-parametric statistics and multivariable regression. Results The study included 135 participants: unilateral unipedicled (n=84), unilateral bipedicled (n=24) and bilateral unipedicled (n=27). Univariate comparison of the three DIEP types showed a significant difference in 12-hour postoperative morphine requirements (P=0.020); bipedicled unilateral patients used significantly less morphine than unipedicled (unilateral) patients at 12 (P=0.005), 24 (P=0.020), and 48 (P=0.046) hours. Multivariable regression comparing these two groups revealed that both reconstruction type and smoking status were significant predictors for 12-hour postoperative morphine usage (P=0.038 and P=0.049, respectively), but only smoking, remained significant at 24 (P=0.010) and 48 (P=0.010) hours. Bilateral reconstruction patients’ mean hospital stay was 2 days longer than either unilateral reconstruction (P<0.001). Conclusions Although all three forms of DIEP flap breast reconstruction had similar postoperative pain measures, a novel finding of our study was that bipedicled DIEP flap harvest might be associated with lower early postoperative morphine requirements. Bilateral and bipedicled procedures in appropriate patients might therefore be undertaken without significantly increased pain/morbidity compared to unilateral unipedicled reconstructions.
How Should We Assess Pain: Do Patients Prefer a Quantitative or Qualitative Scale? A Study of Patient Preferences

Background: Pain perception is a subjective experience and is influenced by a variety of factors. Pain assessment tools, included the numeric pain rating scale (NRS) and the visual analog scale (VAS). A VAS qualitative (VASQ) scale asks patients their current pain level along a continuum of “Good Day,” “Average Day,” or “Bad Day. ” We had patients complete both scales and asked them their preference and reason for their choice. Methods: We identified patients 18 years of age and older, seen by Palliative medicine at Geisinger, who had cancer-associated pain of at least one-month duration. Patients filled out the study questionnaire composed of 2 questions. Characteristics of patients who preferred the VASQ were compared to those who preferred the NRS using a 2-sample t tests or Wilcoxon rank-sum tests and Pearson χ2 or Fisher exact tests. The relationship between the NRS and the VASQ used the Pearson correlation coefficient. Results: One hundred forty-six patients completed the questionnaire, 52.1% were female; 63.7% preferred the NRS, 31.5% preferred the VASQ. Patients who preferred the NRS reported a higher NRS rating than patients who preferred the VASQ (mean NRS rating of 6.0 compared to 5.3) but the difference was not statistically significant (P = .1531). Visual analog scale qualitative ratings were higher among patients who preferred the NRS, but the difference was not statistically different (mean rating of 5.2 vs 4.8, P = .3669). Conclusion: Patients preferred the NRS over VASQ for pain assessment. Patients tend to rate their pain at a higher level when using NRS compared to VASQ.
Essential and sex-specific effects of mGluR5 in ventromedial hypothalamus regulating estrogen signaling and glucose balance

Significance Neural circuits in the ventromedial hypothalamus (VMH) play paramount roles mediating glycemic control and lipid metabolism. Work described in this manuscript reveals a sex-specific role of metabotropic glutamate receptor subtype 5 (mGluR5) mediating these effects. It shows that mGluR5 is required in female but not in male VMH to promote activity of SF1+ neurons in this region and glucose and lipid balance control. Importantly, it demonstrates that mGluR5 modulates the effects of estrogen on activity of SF1+ neurons and glycemic control, which switch from faciliatory and protective to deleterious in the absence of this glutamate receptor. The results inform an essential central mechanism regulating metabolic function in females and underlying the protective effects of estrogen against metabolic disease. The ventromedial hypothalamus (VMH) plays chief roles regulating energy and glucose homeostasis and is sexually dimorphic. We discovered that expression of metabotropic glutamate receptor subtype 5 (mGluR5) in the VMH is regulated by caloric status in normal mice and reduced in brain-derived neurotrophic factor (BDNF) mutants, which are severely obese and have diminished glucose balance control. These findings led us to investigate whether mGluR5 might act downstream of BDNF to critically regulate VMH neuronal activity and metabolic function. We found that mGluR5 depletion in VMH SF1 neurons did not affect energy balance regulation. However, it significantly impaired insulin sensitivity, glycemic control, lipid metabolism, and sympathetic output in females but not in males. These sex-specific deficits are linked to reductions in intrinsic excitability and firing rate of SF1 neurons. Abnormal excitatory and inhibitory synapse assembly and elevated expression of the GABAergic synthetic enzyme GAD67 also cooperate to decrease and potentiate the synaptic excitatory and inhibitory tone onto mutant SF1 neurons, respectively. Notably, these alterations arise from disrupted functional interactions of mGluR5 with estrogen receptors that switch the normally positive effects of estrogen on SF1 neuronal activity and glucose balance control to paradoxical and detrimental. The collective data inform an essential central mechanism regulating metabolic function in females and underlying the protective effects of estrogen against metabolic disease.
Understanding the migration ecology of European red admirals Vanessa atalanta using stable hydrogen isotopes

Tracking migratory movement of small animals with variable migration patterns is difficult with standard mark-recapture methods or genetic analysis. We used stable hydrogen isotope (delta D) measurements of wings from European red admirals Vanessa atalanta to study several aspects of this species' migration. In the central part of southern Europe we found large differences in delta D values between red admirals sampled in autumn and spring supporting the hypothesis that reproduction takes place in the Mediterranean region during winter. There was also an apparent influx to southern Europe in the spring of individuals with a more southerly origin, since many samples had higher delta D values and similar to those expected from coastal areas of North Africa. We found a clear seasonal difference in the delta D values of red admirals sampled in northern Europe. Spring migrants arriving in northern Europe generally had high delta D values that indicated a southerly origin. In autumn, delta D values suggested that red admirals were mostly from regions close to the sampling sites, but throughout the sampling period there were always individuals with delta D values suggesting non-local origins. The migration pattern of this species is supposedly highly variable and plastic. delta D differences between individuals in the western part of Europe were generally small making migratory patterns difficult to interpret. However, butterflies from western Europe were apparently isolated from those from north-eastern Europe, since delta D values in the western region rarely corresponded to those of autumn migrants from the north-east. Use of delta D data for inferring butterfly migration in Europe is complex, but our study showed that this technique can be used to help uncover previously unknown aspects of red admiral migration. (Less)
Prognostic value of novel immune-related genomic biomarkers identified in head and neck squamous cell carcinoma

Background The immune response within the tumor microenvironment plays a key role in tumorigenesis and determines the clinical outcomes of head and neck squamous cell carcinoma (HNSCC). However, to date, a paucity of robust, reliable immune-related biomarkers has been identified that are capable of estimating prognosis in HNSCC patients. Methods High-throughput RNA sequencing was performed in tumors and matched adjacent tissues from five HNSCC patients, and the immune signatures expression of 730 immune-related transcripts selected from the nCounter PanCancer Immune Profiling Panel were assessed. Survival analyzes were performed in a training cohort, consisting of 416 HNSCC cases, retrieved from The Cancer Genome Atlas (TCGA) database. A prognostic signature was built, using elastic net-penalized Cox regression and backward, stepwise Cox regression analyzes. The outcomes were validated by an independent cohort of 115 HNSCC patients, using tissue microarrays and immunohistochemistry staining. Cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) was also used to estimate the relative fractions of 22 immune-cell types and their correlations coefficients with prognostic biomarkers. Results Collectively, 248 immune-related genes were differentially expressed in paired tumors and normal tissues using RNA sequencing. After process screening in the training TCGA cohort, four immune-related genes (PVR, TNFRSF12A, IL21R, and SOCS1) were significantly associated with overall survival (OS). Integrating these genes with Path_N stage, a multiplex model was built and suggested better performance in determining 5 years OS (receiver operating characteristic (ROC) analysis, area under the curve (AUC)=0.709) than others. Further protein-based validation was conducted in 115 HNSCC patients. Similarly, high expression of PVR and TNFRSF12A were associated with poor OS (Kaplan-Meier p=0.017 and 0.0032), while high expression of IL21R and SOCS1 indicated favorable OS (Kaplan-Meier p<0.0001 and =0.0018). The integrated model with Path_N stage still demonstrated efficacy in OS evaluation (Kaplan-Meier p<0.0001, ROC AUC=0.893). Besides, the four prognostic genes were significantly correlated with activated CD8+ T cells, CD4+ T cells, follicular helper T cells and regulatory T cells, implying the possible involvement of these genes in the immunoregulation and development of HNSCC. Conclusions The well-established model encompassing both immune-related biomarkers and clinicopathological factor might serve as a promising tool for the prognostic prediction of HNSCC.