Miracle-dz/UniFAR-FTUs huggingface dataset:
An Alginate-Based Hydrogel with a High Angiogenic Capacity and a High Osteogenic Potential

In bone tissue engineering, autologous cells are combined with osteoconductive scaffolds and implanted into bone defects. The major challenge is the lack of post-implantation vascular growth into biomaterial. The objective of the present study was to develop a new alginate-based hydrogel that enhances the regeneration of bone defects after surgery. The viability of human bone marrow-derived mesenchymal stem cells (BM-MSCs) or human endothelial cells (ECs) cultured alone or together on the hydrogel was analyzed for 24 and 96 h. After seeding, the cells self-assembled and aggregated to form clusters. For functional validation, empty or cellularized hydrogel matrices were implanted ectopically at subcutaneous sites in nude mice. After 2 months, the matrices were explanted. Transplanted human cells were present, and we observed vessels expressing human von Willebrand factor (resulting from the incorporation of transplanted ECs into neovessels and/or the differentiation of BM-MSCs into ECs). The addition of BM-MSCs improved host vascularization and neovessel formation from human cells, relative to ECs alone. Although we did not observe bone formation, the transplanted BM-MSCs were able to differentiate into osteoblasts. This new biomaterial provided an appropriate three-dimensional environment for transplanted cells and has a high angiogenic capacity and an osteogenic potential.
Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families

Validation of a Novel Expressed Sequence Tag (EST) Clustering Method and Development of a Phylogenetic Annotation Pipeline for Livestock Gene Families. (December 2008) Anand Venkatraman, B.Pharm. , The Tamil Nadu Dr. MGR Medical University; M.Tech., Jadavpur University Co-Chairs of Advisory Committee: Dr. James C. Hu Dr. Christine G. Elsik Prediction of functions of genes in a genome is a key step in all genome sequencing projects. Sequences that carry out important functions are likely to be conserved between evolutionarily distant species and can be identified using crossspecies comparisons. In the absence of completed genomes and the accompanying highquality annotations, expressed sequence tags (ESTs) from random cDNA clones are the primary tools for functional genomics. EST datasets are fragmented and redundant, necessitating clustering of ESTs into groups that are likely to have been derived from the same genes. EST clustering helps reduce the search space for sequence homology searching and improves the accuracy of function predictions using EST datasets. This dissertation is a case study that describes clustering of Bos taurus and Sus scrofa EST datasets, and utilizes the EST clusters to make computational function predictions using a comparative genomics approach.
Molecular phylogeny of Sterrhinae moths (Lepidoptera: Geometridae): towards a global classification

A multigene phylogenetic study was carried out to test current, mostly morphology‐based hypotheses on Sterrhinae phylogeny with additional material included from further geographical areas and morphologically different lineages. A maximum likelihood analysis (11 molecular markers and 7665 bp) was conducted on 76 species and 41 genera using iq‐tree software. The resulting phylogenetic hypothesis is well resolved and branches have high support values. Results generally agree with earlier hypotheses at tribal levels and support the hypothesis that Sterrhinae comprises two major lineages. Based on the molecular phylogeny and extensive morphological examination, nine tribes are considered valid and the following taxonomic changes are introduced to recognize monophyletic groups: Mecoceratini Guenée, 1858 (= Ametridini Prout, 1910) is transferred from Desmobathrinae to Sterrhinae, and it is considered valid at tribal level new classification; Haemaleini Sihvonen & Brehm is described as a new tribe and deemed sister to Scopulini + Lissoblemmini; Lissoblemmini Sihvonen & Staude is described as a new tribe and sister to Scopulini; Lythriini Herbulot, 1962 is now a junior synonym of Rhodometrini Agenjo, 1952 syn.n. ; and Rhodostrophiini Prout, 1935 is now a junior synonym of Cyllopodini Kirby, 1892 syn.n. In addition, 48 taxa are transferred from other geometrid subfamilies to Sterrhinae, or within Sterrhinae from one tribe to another, or they are classified into a tribe for the first time, or a new genus classification is proposed. The results demonstrate the limited explanatory power of earlier classifications, particularly at the tribal level. This is probably a result of earlier classifications being based on superficial characters and biased towards the European and North American fauna. The species richness and distribution of Sterrhinae and its constituent tribes are reviewed, showing that the globally distributed Sterrhinae are most diverse in the Neotropics (31% of global fauna). They are species‐rich in the Palaearctic (22%), Afrotropics (19%) and Indo‐Malay (16%) regions, whereas they are almost absent in Oceania (1%). In terms of the described fauna, the most species‐rich tribes are Scopulini (928 species), Sterrhini (876 species) and Cosymbiini (553 species), all of which have a cosmopolitan distribution. Mecoceratiini and Haemaleini are almost entirely Neotropical. Timandrini and Lissoblemmini, by contrast, are absent in the Neotropics. We present a revised classification of the global Sterrhinae fauna, which includes about 3000 putatively valid species, classified into nine tribes and 97 genera. Four genera are of uncertain position within Sterrhinae. Our results highlight the compelling need to include more genera from a global perspective in molecular phylogenetic studies, in order to create a stable global classification for this subfamily.
Absorption of immunoglobulin from colostrum in newborn calves.

One hundred and forty-one calves, belonging to three different breeds, were each given one single feeding of a variable amount of colostrum from their dams at the age of 2, 6, 10, 14 or 20 hr, respectively. The increase in serum Ig concentration during the first 24 hr after colostrum feeding (Δ Ig % 24) was a function of the mass of Ig fed to the calf, the age at colostrum feeding, and the birth weight of the calf. Among these three factors the mass of Ig and the age of the calf were the two predominant factors. The absorption coefficient, expressing the absorbed fraction of a given amount of Ig, was primarily determined by the age of the calf at first feeding. Thus the absorption coefficient was reduced linearly to about half by delaying the feeding from 2 to 20 hr. Except for a negative effect of increasing amounts of colostrum in one of the breeds, no other factors were detected as responsible for variation in the efficiency of Ig absorption. Thus, the absorption coefficient appeared to be unaffected by the Ig % in the colostrum and also by the quantity of Ig given to the calf.
QUANTIFYING HOME-RANGE OVERLAP: THE IMPORTANCE OF THE UTILIZATION DISTRIBUTION

Abstract The concept of an animal's home range has evolved over time, as have methods for estimating home-range size and shape. Recently, home-range estimation methods have focused on estimating an animal's utilization distribution (UD; i.e., the probability distribution defining the animal's use of space). We illustrate the importance of the utilization distribution in characterizing the degree of overlap between home ranges (e.g., when assessing site fidelity or space-use sharing among individuals). We compare several different statistics for their ability to accurately rank paired examples in terms of their degree of overlap. These examples illustrate limitations of indices commonly used to quantify home-range overlap and suggest that new overlap indices that are a function of the UD are likely to be more informative. We suggest 2 new statistics for measuring home-range overlap: (1) for a measure of space-use sharing, we suggest a generalization of Hurlbert's (1978) E/Euniform statistic, which we term the utilization distribution overlap index (UDOI), and (2) for a general measure of similarity between UD estimates, we suggest Bhattacharyya's affinity (BA; Bhattacharyya 1943). Using a short simulation study, we found that overlap indices can accurately rank pairs of UDs in terms of the extent of overlap, but estimates of overlap indices are likely to be biased. The extent of the bias depended on sample size and the degree of overlap (UDs with a high degree of overlap resulted in statistics that were more biased [low]), suggesting that comparisons across studies may be problematic. We illustrate the use of overlap indices to quantify the degree of similarity among UD estimates obtained using 2 different data collection methods (Global Positioning Systems [GPS] and very high frequency [VHF] radiotelemetry) for an adult female northern white-tailed deer (Odocoileus virginianus) in north-central Minnesota.
Demystifying the Effects of Age at Marriage and Age at First Birth on Completed Family Size in Zambia

The link between age at marriage and first birth in explaining completed family size is not always direct, due to heterogeneity in circumstances, that compel individual women to marry or initiate childbearing at a particular age. We analyzed data for 1020 women aged 45-49 in 2014 of the 1965-1969 birth cohort from the 2013-14 ZDHS. We fitted a bivariate and multivariate multinomial logistic regression to establish the effect of mother’s age at first marriage and at first birth on completed family size (CFS). Chi-square test of proportions measuring differences in proportions and relative risk ratios (RRR) with confident intervals at 95% are reported. Our results show that the average CFS was 6.7 (95% CI: 6.5 – 6.9) among women completing their reproductive span in 2014 with mean age at first marriage and birth being 18.3 years (95% CI: 18.0 – 18.5) and 18.9 years (95% CI: 18.7 – 19.1) respectively. Women marrying at younger ages and having their first birth at younger ages were more likely (RRR: 0.262; 95% CI:0.126-0.547 and RRR: 0.176; 95% CI:0.068-0.497 respectively) to have higher CFS than their compatriots that initiated both marriage and childbearing at or after age 22. Having no education, being a rural resident and having a medium household wealth all increased the risk of having higher CFS. Women that marry before age 19 have a higher likelihood of having 6 or more children by the end of their reproductive period. The study concludes that apart from a woman’s age at first marriage and first birth, a complex network of factors interact to determined CFS.
Short-term Peginterferon-Induced High Functional Cure Rate in Inactive Chronic Hepatitis B Virus Carriers With Low Surface Antigen Levels

Abstract Background None of the current guidelines recommend antiviral therapy for inactive hepatitis B virus (HBV) carriers (IHCs). Methods In this real-world, multicenter, nonrandomized study, 32 participants meeting the inclusion criteria were enrolled 1:1 for treatment with peginterferon α-2b or monitoring without treatment based on participant preference. The expected treatment duration was 48 weeks. The primary end point was hepatitis B surface antigen (HBsAg) loss. The HBV vaccine could be injected after HBsAg loss. Results All patients had HBsAg levels of <20 IU/mL. The mean baseline HBsAg levels were 6.6 IU/mL and 5.8 IU/mL in the treated and untreated groups, respectively. Fifteen (93.8%) participants achieved HBsAg loss, 5 obtained HBsAg seroconversion after undergoing a mean of 19.7 weeks of therapy in the treated group, and no one in the follow-up group achieved HBsAg loss during a mean follow-up time of 12.6 months (P < .0001). Generally, the therapy was well tolerated. Nine of 11 individuals who exhibited HBsAg loss benefited from receiving the HBV vaccine. Conclusions This study provides justification for further studies of short-course peginterferon α-2b for the functional cure of IHCs with low HBsAg levels. Additionally, HBV vaccine injection is beneficial after interferon-induced HBsAg loss.
Encounter rate between local populations shapes host selection in complex parasite life cycle

The present study aimed to understand how a parasite with a complex life cycle selects a given host succession when several potential hosts are present. Ligula intestinalis (Cestoda, Pseudophyllidea) was considered, which presents a life cycle with three hosts: copepod, fish, and piscivorous bird. Encounter probability between each pair of hosts was calculated for Lavernose-Lacasse gravel pit (France) using a sum of the product of the host abundances over time. Among four potential copepod hosts, two potential fish hosts, and six potential bird hosts, the results demonstrate that the copepod Eudiaptomus gracilis, the roach (Rutilus rutilus), and the great crested grebe (Podiceps cristatus) had a maximal encounter probability due to their abundance, but also due to the similarities of the temporal dynamics of their life cycles. These results agree with previous experiments and field work identifying a high specificity of L. intestinalis to E. gracilis, R. rutilus, and P. cristatus in the study site. This suggests that the abundance of potential hosts and the temporal dynamics of their life cycles act together to determine encounter rates between hosts and parasites, and thus could constitute a crucial determinant in local host selection by parasites with a complex life cycle. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89, 99–106.
Recognizing the 3‐Sphere

All manifolds in this paper are piecewise linear and are given in terms of a finite triangulation. In dimensions 5 3 this is completely general by virtue of the Moise triangulation theorem. By a closed manifold we mean a manifold that is connected, compact, and without boundary. The homeomorphism problem-to decide whether two closed manifolds are homeomorphic-is solved in dimensions 1 and 2 and, in general, unsolvable [9] in dimensions 24 . In three-dimensions, even the existence of an algorithm for deciding whether a manifold is a sphere, is open. In this paper the question for the 3-sphere is approached combinatorially, and an algorithm for recognizing the 3-sphere is conjectured. In 1904 PoincarC proved that the Betti and torsion numbers do not suffice to determine the 3-sphere among closed 3-manifolds and conjectured that the 3-sphere is characterized by being simply connected. An affirmative answer to the PoincarC conjecture would reduce the problem of recognizing the 3-sphere to the problem of determining algorithmically whether the fundamental group of a closed 3-manifold is trivial. This is also an open question. Let A be a potential algorithm for recognizing the 3-sphere. To confirm that A is valid, the following statements must be proved.
Impact of weighted rainfalls on the yield of wheat in the Punjab, Pakistan.

A study of weighted rainfalls, which is almost unprecedented effort in agricultural statistics, was conducted to develop a mechanism to assign weights to different amounts of rainfalls proportional to their importance/need of time with reference to the crop condition. It is a methodology for determination of weights assigned to amounts of rainfalls of different months of Rabi season that have a significant impact on the yield of wheat crop. The data of rainfalls from 2000 - 2001 to 2006 - 2007 at seven observatories of Meteorological Department, Punjab and wheat production of respective districts were used. It was observed that as the rainfalls in the important months of Rabi season are increased; the average yield of wheat also increases. But at a certain level, excess rainfalls cause a decline in the yield. The suitable quadratic models were fitted independently between yield and amount of rainfalls for each month of the season. In each case explained variation R² was used as a proposed weight to the rainfall of the relevant Rabi month. The empirical study supported the use of weighted rainfalls instead of total rainfalls of Rabi season. The concept of weighted rainfall was also proved effective in estimating the crop production through a statistical model. Key words: Barani area, district, division, kharif season, maund, rabi season.
EXPLORING QSAR FOR THE INHIBITORY ACTIVITY OF A LARGE SET OF AROMATIC /HETEROCYCLIC SULFONAMIDES TOWARD FOUR DIFFERENT ISOENZYMES OF CARBONIC ANHYDRASE

The Carbonic Anhydrase (CA) inhibitory activities of a large number of sulfonamide derivatives toward CA isoenzyme types I, II, IV, and IX were collected and then subjected to QSAR analyses. The dataset used consisted of 343 sulfonamide derivatives with 200 calculated descriptors. For each type of isoenzyme, a separate QSAR model was obtained using multiple linear regression analysis with stepwise selection of variables. The generalization, stability, and predictivity of the models were evaluated by leave-many-out cross-validation, using an external test set and chance correlation. All the obtained models represented high statistical quality and prediction ability with q2 and greater than 0.80. The relative errors of prediction were lower than 5%. By the developed models, the ligand–receptor interactions involved in the binding of sulfonamides to different CA isoenzymes were discussed. For all types of isoenzymes, the topological indices represented significant impacts on the ligand–enzyme interactions. It was found that, for CAI, the acid–base properties play a significant role whereas for CAII the coulombic interactions are controlling factors. In addition, number of thiol functional groups exhibited significant negative effect on the binding of sulfonamides to CAII. For CAIV, the hydrogen bonding interactions were detected as a major factor. Finally, for the binding of sulfonamides to CAIX, the lipophilicity, and acid–base properties were selected as highly influential parameters.
APECED‐Associated Hepatitis: Clinical, Biochemical, Histological and Treatment Data From a Large, Predominantly American Cohort

Autoimmune polyendocrinopathy‐candidiasis‐ectodermal dystrophy (APECED), caused by autoimmune regulator (AIRE) mutations, manifests with chronic mucocutaneous candidiasis (CMC) and multisystem autoimmunity, most often hypoparathyroidism (HP) and adrenal insufficiency (AI). European cohorts previously reported a ~10% prevalence of APECED‐associated hepatitis (APAH) with presentations ranging from asymptomatic laboratory derangements to fatal fulminant hepatic failure. Herein, we characterized APAH in a large APECED cohort from the Americas.
Macrophage hypophagia as a mechanism of innate immune exhaustion in mAb-induced cell clearance.

Macrophage antibody dependent cellular phagocytosis (ADCP) is a major cytotoxic mechanism for both therapeutic unconjugated monoclonal antibodies (mAb) such as rituximab, and antibody induced hemolytic anemia and immune thrombocytopenia. Here, we studied the mechanisms controlling the rate and capacity of macrophages to carry out ADCP in settings of high target to effector cell ratio such as that seen in patients with circulating tumor burden in leukemic phase disease. Using quantitative live-cell imaging of primary human and mouse macrophages we found that, upon initial challenge with mAb-opsonized lymphocytes, macrophages undergo a brief burst (<1hr) of rapid phagocytosis which is then invariably followed by a sharp reduction in phagocytic activity that can persist for days. This previously unknown refractory period of ADCP, or "hypophagia," was observed in all macrophage/mAb/target cell conditions tested in vitro, and was also seen in vivo in Kupffer cells from mice induced to undergo successive rounds of ⍺CD20 mAb-dependent clearance of circulating B cells. Importantly, hypophagia had no effect on antibody-independent phagocytosis and did not alter macrophage viability. In mechanistic studies we found that the rapid loss of activating Fc receptors from the surface and their subsequent proteolytic degradation is the primary mechanism responsible for the loss of ADCP activity in hypophagia. These data suggest hypophagia is a critical limiting step in macrophage-mediated clearance of cells via ADCP and that understanding such limitations to innate immune system cytotoxic capacity will aid in the development of mAb regimens that could optimize ADCP and improve patient outcome.
Seasonal dynamics of dissolved organic carbon, nitrogen and other nutrients in soil of Pinus massoniana stands after pine wilt disease disturbance

To understand changes in soil nutrients in Pinus massoniana forests affected by pine wilt disease (PWD), we examined the seasonal variation in dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and soil nutrients in Hefei, East China. The results showed a considerable decline in the population density and basal area in both highly disturbed (HD) and moderately disturbed (MD) forest stands and an increase in dead pine trees, causing pronounced changes in the stand structure and soil nutrient status. The concentrations of DOC and NO3-- N were significantly (p < 0.05) higher in every season in the disturbed forests compared to the undisturbed (UD) forest stand. However, during spring and summer, the variation in the DON and NH4+-N values was significantly (p < 0.05) lower in the HD forest stand than in the UD stand; total N concentrations were higher in the disturbed forests in every season. During spring and autumn, the variation in total P values was significantly (p < 0.05) lower in the MD forest stand than in the UD stand, whereas the total P values were significantly (p < 0.05) lower in every season in the HD stand than in the UD stand. In this study, disturbance resulted in a considerable increase in DOC, N and NO3-- N when compared to the UD stand and a pronounced increase in soil nitrate in the HD stand, which may lead to soil acidification, thereby increasing the possibility of soil nutrient leaching.
Path coefficient and correlation of yield and yield associated traits in candidate bread wheat (Triticum aestivum L.) lines.

Yield and yield contributing traits were studied in candidate bread wheat lines in order to find out the genetic contribution of different characters towards grain yield at NIFA, Peshawar, Pakistan during 2001-02. All the characteristics studied differed significantly from one another. Days to heading showed negative and significant correlation with harvest index and grain yield was not found with the biological yield. Days to maturity were negatively correlated at both genotypic and phenotypic levels with biological yield, harvest index and grain yield and the level of negative genotypic correlation was significant with harvest index and grain yield. Plant height showed negative genotypic and phenotypic correlation with harvest index and grain yield. Biological yield had positive significant genotypic and phenotypic correlation with harvest index and grain yield. Harvest index had positive and highly significant genotypic and phenotypic correlation with grain yield. Positive direct effect of days to heading, days to maturity and biological yield with grain yield were observed. Harvest index showed positive and highest direct effect on grain yield. Genotypic and phenotypic correlation coefficients revealed that important characters influencing grain yield (kg/ha) are harvest index and biological yield. Path analysis showed the importance in order of harvest index, biological yield, plant height, days to maturity and days to heading in grain yield.