Miracle-dz/UniFAR-FTUs huggingface dataset:
A Water Quality Appraisal of Some Existing and Potential Riverbank Filtration Sites in India

There is a nationwide need among policy and decision makers and drinking water supply engineers in India to obtain an initial assessment of water quality parameters for the selection and subsequent development of new riverbank filtration (RBF) sites. Consequently, a snapshot screening of organic and inorganic water quality parameters, including major ions, inorganic trace elements, dissolved organic carbon (DOC), and 49 mainly polar organic micropollutants (OMPs) was conducted at 21 different locations across India during the monsoon in June–July 2013 and the dry non-monsoon period in May–June 2014. At most existing RBF sites in Uttarakhand, Jammu, Jharkhand, Andhra Pradesh, and Bihar, surface and RBF water quality was generally good with respect to most inorganic parameters and organic parameters when compared to Indian and World Health Organization drinking water standards. Although the surface water quality of the Yamuna River in and downstream of Delhi was poor, removals of DOC and OMPs of 50% and 13%–99%, respectively, were observed by RBF, thereby rendering it a vital pre-treatment step for drinking water production. The data provided a forecast of the water quality for subsequent investigations, expected environmental and human health risks, and the planning of new RBF systems in India.
Functional convergence and phylogenetic divergence during secondary succession of subtropical wet forests in Puerto Rico

Question Understanding how the relative importance of different community assembly processes changes during secondary succession of diverse systems remains elusive. Functional and phylogenetic approaches that place species along continuous axes of niche differentiation and evolutionary relatedness, however, are deepening our understanding of the mechanisms that drive successional dynamics. We ask whether successional shifts in the functional and phylogenetic composition of post-agricultural tropical forests provide evidence for niche partitioning or competitive dominance hierarchies as drivers of successional change. Location Subtropical wet forests, Puerto Rico. Methods We combined data on four functional traits [leaf dry mass per area (LMA), wood density (WD), maximum height (Hmax), seed dry mass] and a well-resolved molecular phylogeny to characterize taxonomic, functional and phylogenetic composition of sapling and adult tree communities along a regionally replicated chronosequence. We used a null model approach to assess how functional and phylogenetic diversity change with forest age. Results Corresponding increases of community-weighted mean LMA, Hmax and seed mass with forest age reflected a shift in dominance of species with acquisitive resource-use strategies and small seeds towards species with more conservative resource use and larger seeds. A negative relationship between forest age and local diversity of Hmax and seed mass suggested increased importance of competitive hierarchies for light capture and shade-tolerant regeneration in older forests. In contrast, the colonization of palms in older forest plots led to a positive relationship between forest age and local phylogenetic diversity, suggesting functional convergence of distantly related lineages on traits that confer competitive dominance under low resource conditions. Conclusions We linked both functional and phylogenetic dimensions of community diversity with successional trajectories of post-agricultural tropical forests. Contrasting patterns of these dimensions of diversity shed light on the underlying community assembly processes. We argue that integrating traits and phylogeny with specific hypotheses about physiological and historical mechanisms is essential for advancing our understanding of the drivers of community change during succession.
Functional Genomics of 5- to 8-Cell Stage Human Embryos by Blastomere Single-Cell cDNA Analysis

Blastomere fate and embryonic genome activation (EGA) during human embryonic development are unsolved areas of high scientific and clinical interest. Forty-nine blastomeres from 5- to 8-cell human embryos have been investigated following an efficient single-cell cDNA amplification protocol to provide a template for high-density microarray analysis. The previously described markers, characteristic of Inner Cell Mass (ICM) (n = 120), stemness (n = 190) and Trophectoderm (TE) (n = 45), were analyzed, and a housekeeping pattern of 46 genes was established. All the human blastomeres from the 5- to 8-cell stage embryo displayed a common gene expression pattern corresponding to ICM markers (e.g., DDX3, FOXD3, LEFTY1, MYC, NANOG, POU5F1), stemness (e.g., POU5F1, DNMT3B, GABRB3, SOX2, ZFP42, TERT), and TE markers (e.g., GATA6, EOMES, CDX2, LHCGR). The EGA profile was also investigated between the 5-6- and 8-cell stage embryos, and compared to the blastocyst stage. Known genes (n = 92) such as depleted maternal transcripts (e.g., CCNA1, CCNB1, DPPA2) and embryo-specific activation (e.g., POU5F1, CDH1, DPPA4), as well as novel genes, were confirmed. In summary, the global single-cell cDNA amplification microarray analysis of the 5- to 8-cell stage human embryos reveals that blastomere fate is not committed to ICM or TE. Finally, new EGA features in human embryogenesis are presented.
Accuracy of physical activity monitors in pregnant women.

PURPOSE To determine the step count accuracy of three pedometers and one accelerometer in pregnant women during treadmill walking. METHODS Participants were 30 women in the second or third trimester (20-34 wk) who were screened for pregnancy-related risk factors. Each participant was fitted with a belt containing three physical activity monitors: Yamax Digiwalker SW-200 (DW), New Lifestyles NL 2000 (NL), and GT3X ActiGraph accelerometer (ACT). The Omron HJ-720ITC (HJ) was placed in the pants' front pocket. Participants walked at 54, 67, 80, and 94 m · min for 2 min each. Actual steps were determined by an investigator using a hand-tally counter. The mean percent of steps recorded was calculated for each device at each speed and compared. Pearson correlations were used to determine the effect of body mass index and tilt angle on pedometer accuracy. RESULTS There was a significant interaction between speed and device (F9,20 = 7.574, P < 0.001). Across all speeds, the NL and HJ had the lowest error. The ACT and DW underestimated the actual steps taken, particularly at the slower walking speeds. At 54 m · min, the ACT averaged 77.5% of steps and the DW averaged 56.9% of steps. Significant differences in the mean percent of steps recorded were found between devices at all speeds. Body mass index was only significantly correlated with percent of steps recorded by the NL, and there were no significant correlations between steps recorded and tilt angle. CONCLUSIONS In pregnant women, the ACT and DW had more error than the NL and HJ. On the basis of these results, the NL and HJ should be considered for use in further research studies and physical activity programs that focus on walking during pregnancy.
Susceptibility to three pyrethroids and detection of knockdown resistance mutation in Ghanaian Anopheles gambiae sensu stricto

Abstract Although insecticides play a crucial role in malaria control programs, this strategy is threatened by the development of resistance in the vectors to commonly used public health insecticides. Due to their known efficacy and lower toxicity to humans and non-target organisms, pyrethroids have been used in many vector control projects. In West Africa, pyrethroid resistance in the major malaria vector, Anopheles gambiae, had been reported in several countries. It was, therefore, imperative to investigate the susceptibility of this very important malaria vector in Ghana and characterize the resistance mechanism. Larvae of Anopheles gambiae sensu lato were collected from rural and urban sites and reared to adults. Species identification was by morphological characteristics, PCR, and HhaI restriction digest. Female mosquitoes that were two to three days old were selected and exposed to World Health Organization (WHO) diagnostic doses of three pyrethroids. A susceptible laboratory strain of An. gambiae sensu stricto was used as a reference. Both survivors and dead mosquitoes from bioassays were screened for the knockdown resistance mutation. An. gambiae sensu stricto was the only sibling species of the complex present in these localities with the molecular S form being predominant (>95%). Resistance to pyrethroids up to 8.5 fold was observed, with very high kdr frequency. The relative ease in using molecular techniques has resulted in rapid detection of ostensible insecticide resistance genes in malaria vectors. However, it is even more important to complement these molecular tools with routine insecticide testing in the field, especially if the insecticides are earmarked for public health use.
Complete Suppression of Tumor Formation by High Levels of Basement Membrane Collagen

Suppression of tumorigenicity was first shown in hybrids produced by the fusion of a range of different highly malignant tumor cells with diploid fibroblasts. Cytogenetic analysis of these hybrids revealed that suppression involved a genetic region located in one specific chromosome donated to the hybrid cell by the fibroblast parent. The identity of the gene responsible for this dramatic effect has remained obscure. We now present strong evidence that the primary determinant is the gene specifying collagen XV, a proteoglycan closely associated with the basement membrane. We transfected a line of highly tumorigenic human cervical carcinoma cells with an expression vector carrying the full-length cDNA of the human collagen XV gene. We selected clones making various amounts of collagen XV, examined their growth in vitro, and tested their tumorigenicity in nude mice. High levels of collagen XV altered the growth properties of the cells in three-dimensional cultures. Moreover, we found that, in a dose-dependent manner, the production of collagen XV completely suppressed tumorigenicity in clones that synthesized this molecule at high levels. Immunohistologic studies suggest that suppression is associated with extracellular deposition of the proteoglycan at the cell periphery. (Mol Cancer Res 2007;5(12):1241–5)
The Kinematic Effects of the Defects in Liquid Crystal Dynamics

Here we investigate the kinematic transports of the defects in the nematic liquid crystal system by numerical experiments. The model is a shear flow case of the viscoelastic continuum model simplified from the Ericksen-Leslie system. The numerical experiments are carried out by using a difference method. Based on these numerical experiments we find some interesting and important relationships between the kinematic transports and the characteristics of the flow. We present the development and interaction of the defects. These results are partly consistent with the observation from the experiments. Thus this scheme illustrates, to some extent, the kinematic effects of the defects. AMS subject classifications: 65M70, 76A15
Emergence of online communities: Empirical evidence and theory

Online communities, which have become an integral part of the day-to-day life of people and organizations, exhibit much diversity in both size and activity level; some communities grow to a massive scale and thrive, whereas others remain small, and even wither. In spite of the important role of these proliferating communities, there is limited empirical evidence that identifies the dominant factors underlying their dynamics. Using data collected from seven large online platforms, we observe a relationship between online community size and its activity which generally repeats itself across platforms: First, in most platforms, three distinct activity regimes exist—one of low-activity and two of high-activity. Further, we find a sharp activity phase transition at a critical community size that marks the shift between the first and the second regime in six out of the seven online platforms. Essentially, we argue that it is around this critical size that sustainable interactive communities emerge. The third activity regime occurs above a higher characteristic size in which community activity reaches and remains at a constant and higher level. We find that there is variance in the steepness of the slope of the second regime, that leads to the third regime of saturation, but that the third regime is exhibited in six of the seven online platforms. We propose that the sharp activity phase transition and the regime structure stem from the branching property of online interactions.
Morusin inhibits cell proliferation and tumor growth by down-regulating c-Myc in human gastric cancer

Morusin is a pure extract from the root bark of Morus australis (Moraceae). In recent years, morusin has been reported to exhibit anti-tumor biological activity in some types of human cancers through different mechanisms. Here, we attempted to investigate the inhibitory effect and mechanism of morusin on gastric cancer. Morusin markedly inhibited gastric cancer cell proliferation by down-regulating CDKs and Cyclins, such as CDK2, CDK4, Cyclin D1 and Cyclin E1. Additionally, morusin suppressed tumor growth in vitro and in vivo. Up-regulation of CDKs and Cyclins in gastric cancer cells was induced by c-Myc binding at the E-Box regions of CDKs and the Cyclin promoter. In addition, compared with the control group, the morusin-treated group showed reduced expression of c-Myc and c-Myc protein binding at the E-Box regions. Based on these results, we overexpressed c-Myc in gastric cancer cells and found that overexpressing c-Myc rescued morusin-induced inhibition of cell proliferation and tumor growth. These results suggest that morusin inhibits cell proliferation and tumor growth by down-regulating c-Myc in human gastric cancer.
Ineffectiveness of Reverse Wording of Questionnaire Items: Let’s Learn from Cows in the Rain

Objective We examined the effectiveness of reverse worded items as a means of reducing or preventing response bias. We first distinguished between several types of response bias that are often confused in literature. We next developed arguments why reversing items is probably never a good way to address response bias. We proposed testing whether reverse wording affects response bias with item-level data from the Multidimensional Fatigue Inventory (MFI-20), an instrument that contains reversed worded items. Methods With data from 700 respondents, we compared scores on items that were similar with respect either to content or to direction of wording. Psychometric properties of sets of these items worded in the same direction were compared with sets consisting of both straightforward and reversed worded items. Results We did not find evidence that ten reverse-worded items prevented response bias. Instead, the data suggest scores were contaminated by respondent inattention and confusion. Conclusions Using twenty items, balanced for scoring direction, to assess fatigue did not prevent respondents from inattentive or acquiescent answering. Rather, fewer mistakes are made with a 10-item instrument with items posed in the same direction. Such a format is preferable for both epidemiological and clinical studies.
Optical solitary waves in thermal media with non-symmetric boundary conditions

Optical spatial solitary waves are considered in a nonlocal thermal focusing medium with non-symmetric boundary conditions. The governing equations consist of a nonlinear Schrödinger equation for the light beam and a Poisson equation for the temperature of the medium. Three numerical methods are investigated for calculating the ground and excited solitary wave solutions of the coupled system. It is found that the Newton conjugate gradient method is the most computationally efficient and versatile numerical technique. The solutions show that by varying the ambient temperature, the solitary wave is deflected towards the warmer boundary. Solitary wave stability is also examined both theoretically and numerically, via power versus propagation constant curves and numerical simulations of the governing partial differential equations. Both the ground and excited state solitary waves are found to be stable. The Newton conjugate gradient method should also prove extremely useful for calculating solitary waves of other related optical systems, which support nonlocal spatial solitary waves, such as nematic liquid crystals.
EBEK: Exemplar-Based Kernel Preserving Embedding

With the rapid increase in the available data, it becomes computationally harder to extract useful information. Thus, several techniques like PCA were proposed to embed high-dimensional data into low-dimensional latent space. However, these techniques don't take the data relations into account. This motivated the development of other techniques like MDS and LLE which preserve the relations between the data instances. Nonetheless, all these techniques still use latent features, which are difficult for data analysts to understand and grasp the information encoded in them. In this work, a new embedding technique is proposed to mitigate the previous problems by projecting the data to a space described by few points (i.e, exemplars) which preserves the relations between the data points. The proposed method Exemplar-based Kernel Preserving (EBEK) embedding is shown theoretically to achieve the lowest reconstruction error of the kernel matrix. Using EBEK in approximate nearest neighbor task shows its ability to outperform related work by up to 60% in the recall while maintaining a good running time. In addition, our interpretability experiments show that EBEK's selected basis are more understandable than the latent basis in images datasets.
Female coloration indicates female reproductive capacity in blue tits

It is poorly understood whether female morphological and behavioural traits can be used as ‘signals’. In particular, experimental tests of the hypothesis that female ornaments reflect quality are scarce. Here, we experimentally examine whether female plumage coloration might signal maternal quality in the blue tit, Cyanistes caeruleus by forcing half of the females breeding in our population to produce a replacement clutch. Using statistical models that controlled for the effects of male coloration, and the effects of age and condition of both parents, we found that carotenoid‐based female coloration was positively linked to key proxies of bird lifetime reproductive success: clutch size, fledgling success and recruitment. Importantly, the relationships between maternal yellow carotenoid coloration and both clutch size and recruitment were stronger in the experimental group than in the control group, indicating that breeding females with higher values of yellow coloration were better able to handle the cost of producing a second clutch. Finally, UV‐blue female coloration was positively linked to female survival and marginally linked to laying date. Taken together, these results show for the first time in a natural population that female coloration can indicate individual and maternal quality under natural and adverse reproductive conditions. They highlight the potential for the evolution of female ornamental traits through sexual selection.
Coupling growth-factor engineering with nanotechnology for therapeutic angiogenesis

Therapeutic angiogenesis is an emerging paradigm for the management of ischemic pathologies. Proangiogenic Therapy is limited, however, by the current inability to deliver angiogenic factors in a sustained manner at the site of pathology. In this study, we investigated a unique nonglycosylated active fragment of hepatocyte growth factor/scatter factor, 1K1, which acts as a potent angiogenic agent in vitro and in a zebrafish embryo and a murine matrigel implant model. Furthermore, we demonstrate that nanoformulating 1K1 for sustained release temporally alters downstream signaling through the mitogen activated protein kinase pathway, and amplifies the angiogenic outcome. Merging protein engineering and nanotechnology offers exciting possibilities for the treatment of ischemic disease, and furthermore allows the selective targeting of downstream signaling pathways, which translates into discrete phenotypes.
Research on the cooperative decision of business application needs in IT governance

The decision of business application needs is getting more and more attention because it is the only one to bring commercial value directly in five major decisions of IT governance. However, throughout the methods widely used currently for business application needs decision, some only reflect the wishes and ideas of individual managers and the other are so generalized that cannot provide either business or IT strategy guidance to business modeling. The paper develops a cooperation decision mechanism combining the cluster analysis of P/U matrix with critical success factors which puts forward a new idea for analyzing the business application needs in IT governance implementation. The feasibility of the proposed mechanism is then proved by the application in metro transportation project.
Development of prostate cancer in a patient with primary hypogonadism: intratumoural steroidogenesis in prostate cancer tissues

Intratumoural steroidogenesis may play a significant role in the progression of prostate cancer (PC) in the context of long‐term ablation of circulating testosterone (T). To clarify the mechanism accounting for the progression of PC in a 74‐year‐old man who had undergone bilateral orchiectomy when he was 5 years old, we performed immunohistochemical studies of androgen receptor (AR) and steroidogenic enzymes in the prostate. We also measured steroid hormone levels in the serum and prostate, as well as mRNA levels of genes mediating androgen metabolism in the prostate. Positive nuclear staining of AR was detected in malignant epithelial cells. The levels of androstenedione (Adione), T, and 5‐alpha dihydrotestosterone (DHT) in the serum of the patient were similar to those in PC patients receiving neoadjuvant androgen deprivation therapy (ADT), but were higher in the patient's prostate than in PC patients not receiving ADT. The gene expression of CYP17A1 and HSD3B1 was not detected, whereas that of STS, HSD3B2, AKR1C3, SRD5A1, and SRD5A2 was detected. Moreover, cytoplasmic staining of HSD3B2, AKR1C3, SRD5A1, and SRD5A2 was detected in malignant epithelial cells. Hence, in the present case (a man with primary hypogonadism), steroidogenesis in PC tissues from adrenal androgens, especially dehydroepiandrosterone sulphate, was the mechanism accounting for progression of PC. This mechanism might help elucidate the development of castration‐resistant PC.
Comprehensive analysis of circRNA expression profiles in humans by RAISE

Circular RNAs (circRNAs) are pervasively expressed circles of non-coding RNAs. Even though many circRNAs have been reported in humans, their expression patterns and functions remain poorly understood. In this study, we employed a pipeline named RAISE to detect circRNAs in RNA-seq data. RAISE can fully characterize circRNA structure and abundance. We evaluated inter-individual variations in circRNA expression in humans by applying this pipeline to numerous non-poly(A)-selected RNA-seq data. We identified 59,128 circRNA candidates in 61 human liver samples, with almost no overlap in the circRNA of the recruited samples. Approximately 89% of the circRNAs were detected in one or two samples. In comparison, 10% of the linear mRNAs and non-coding RNAs were detected in each sample. We estimated the variation in other tissues, especially the circRNA high-abundance tissues, in advance. Only 0.5% of the 50,631 brain circRNA candidates were shared among the 30 recruited brain samples, which is similar to the proportion in liver. Moreover, we found inter- and intra-individual diversity in circRNAs expression in the granulocyte RNA-seq data from seven individuals sampled 3 times at one-month intervals. Our findings suggest that careful consideration of inter-individual diversity is required when extensively identifying human circRNAs or proposing their use as potential biomarkers and therapeutic targets in disease.