Miracle-dz/UniFAR-FTUs huggingface dataset:
Foreign-controlled firms in Indian manufacturing: long-term trends *

The extent to which foreign-controlled firms dominate Indian manufacturing has been a matter of some controversy. Existing estimates do not always agree with each other, as they rely on different data sets, methodologies and assumptions. We present estimates based on a Reserve Bank of India study of Medium and Large Companies for the period 1965-1994.
Snakeskin, a membrane protein associated with smooth septate junctions, is required for intestinal barrier function in Drosophila

Septate junctions (SJs) are the membrane specializations observed between epithelial cells in invertebrates. SJs play a crucial role in epithelial barrier function by restricting the free diffusion of solutes through the intercellular space. In arthropod species, two morphologically different types of SJs have been described: pleated septate junctions (pSJs) and smooth septate junctions (sSJs), which are specific to ectodermal and endodermal epithelia, respectively. In contrast to the recent identification of pSJ-related proteins, the molecular constituents of sSJs are mostly unknown. Here, we report the discovery of a new sSJ-specific membrane protein, designated ‘Snakeskin’ (Ssk). Ssk is highly concentrated in sSJs in the Drosophila midgut and Malpighian tubules. Lack of Ssk expression is embryonically lethal in Drosophila and results in defective sSJ formation accompanied by abnormal morphology of midgut epithelial cells. We also show that the barrier function of the midgut to a fluorescent tracer is impaired in ssk-knockdown larvae. These results suggest that Ssk is required for the intestinal barrier function in Drosophila.
DSS‐Induced Colitis Is Exacerbated in STAT‐6 Knockout Mice

Background: Several transcription factors have been proposed to regulate IBD including the signal transducer and activator of transcription‐6 (STAT‐6). Methods: The role of STAT‐6 was examined in the 5% dextran sulfate sodium (DSS)‐induced murine model of colitis using STAT‐6−/− and wildtype mice. Results: The disease activity index (DAI) revealed a significant increase in DAI in STAT‐6−/− mice over STAT‐6+/+ mice given DSS. Both STAT‐6−/− and wildtype mice displayed severe inflammation and crypt damage. Additionally, STAT‐6−/− mice showed significant injury to the proximal colon compared with their littermate controls. Furthermore, STAT‐6−/− mice receiving DSS had dramatically higher levels of serum nitrite/nitrate than all other groups. STAT‐6−/− animals also displayed higher levels of inteferon‐&ggr; than wildtype mice. Conclusions: Because STAT‐6 has been reported to regulate the expression and activity of inducible NO synthase (iNOS), our data suggest that, in DSS colitis, STAT‐6 may modulate iNOS, to limit NO formation and control the extent of inflammation in the colon. We conclude that STAT‐6 may normally play an important regulatory role in the pathogenesis of inflammatory bowel disease, possibly through modulation of iNOS and interferon‐&ggr;.
Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples

Next‐generation sequencing (NGS) technology has extraordinarily enhanced the scope of research in the life sciences. To broaden the application of NGS to systems that were previously difficult to study, we present protocols for processing faecal and swab samples into amplicon libraries amenable to Illumina sequencing. We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater. Compared with the MO BIO PowerSoil Kit, the current standard for the Human and Earth Microbiome Projects, the SPRI‐based method produced comparable 16S rRNA gene PCR amplification from faecal extractions but significantly greater DNA quality, quantity and PCR success for both cloacal and oral swab samples. We furthermore modified published protocols for preparing highly multiplexed Illumina libraries with minimal sample loss and without post‐adapter ligation amplification. Our library preparation protocol was successfully validated on three sets of heterogeneous amplicons (16S rRNA gene amplicons from SPRI and PowerSoil extractions as well as control arthropod COI gene amplicons) that were sequenced across three independent, 250‐bp, paired‐end runs on Illumina's MiSeq platform. Sequence analyses revealed largely equivalent results from the SPRI and PowerSoil extractions. Our comprehensive strategies focus on maximizing efficiency and minimizing costs. In addition to increasing the feasibility of using minimally invasive sampling and NGS capabilities in avian research, our methods are notably not avian‐specific and thus applicable to many research programmes that involve DNA extraction and amplicon sequencing.
Mitogenomic sequences support a north–south subspecies subdivision within Solenodon paradoxus

Abstract Solenodons are insectivores found only in Hispaniola and Cuba, with a Mesozoic divergence date versus extant mainland mammals. Solenodons are the oldest lineage of living eutherian mammal for which a mitogenome sequence has not been reported. We determined complete mitogenome sequences for six Hispaniolan solenodons (Solenodon paradoxus) using next-generation sequencing. The solenodon mitogenomes were 16,454–16,457 bp long and carried the expected repertoire of genes. A mitogenomic phylogeny confirmed the basal position of solenodons relative to shrews and moles, with solenodon mitogenomes estimated to have diverged from those of other mammals ca. 78 Mya. Control region sequences of solenodons from the northern (n = 3) and southern (n = 5) Dominican Republic grouped separately in a network, with FST = 0.72 (p = 0.036) between north and south. This regional genetic divergence supports previous morphological and genetic reports recognizing northern (S. p. paradoxus) and southern (S. p. woodi) subspecies in need of separate conservation plans.
Wine yeast phenomics: A standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions

This work describes the set up of a small scale fermentation methodology for measuring quantitative traits of hundreds of samples in an enological context. By using standardized screw cap vessels, the alcoholic fermentation kinetics of Saccharomyces cerevisiae strains were measured by following the weight loss over time. Preliminary results showed that the kinetic parameters measured are in agreement with those observed in larger scale vats. The small volume used did not impair any analysis of the strain performance. Indeed, this fermentation system was coupled with robotized enzymatic assays and 8 end-point metabolites of enological interest were measured accurately. Moreover, the vessel used offers the possibility to assay 32 volatiles compounds using a headspace solid-phase microextraction coupled to gas chromatography-mass spectrometry approach. Data presented demonstrates that the shaking conditions significantly impacted the mean and the variance of kinetic parameters, primary metabolites, and the production of volatile compounds. This effect was likely due to an enhanced transfer of dissolved oxygen during the first hours of the alcoholic fermentation. To test the efficiency of this experimental design, the phenotypic response of 35 wine industrial starters was measured in five grape juices from the Bordeaux area. A multivariate analysis illustrated that strains were better discriminated by some grape must, than others. The technological performances as well as the phenotypic robustness of these strains was measured and discussed. The optimized methodology developed allows investigating multiple fermentation traits for numerous yeast strains and conditions and greatly contributes in achieving quantitative genetics studies as well as yeast selection programs.
Studies on the Turnover of Procarboxypeptidase B, Its Active Enzyme and the Activation Peptide in the Pig

Recent developments in the treatment of acute pancreatitis have focused on the importance of early determination of the severity of an attack. Measuring levels of activation peptides from pancreatic proenzymes seems to be one way to predict severity. Levels of the activation peptide from procarboxypeptidase B, in both serum and urine on admission, have been shown to correlate to the outcome. To be able to interpret levels of this peptide in serum and urine under normal and in various acute abdominal conditions, we need knowledge about its turnover in the circulation. Procarboxypeptidase B, active carboxypeptidase and the activation peptide were therefore purified from porcine pancreatic juice. These proteins were labelled with 125I or 131I and their turnovers were studied in vivo in the pig. The proenzyme and the activation peptide were eliminated without interaction with any substance in the circulation. The active enzyme was to some degree bound to a substance with a molecular mass of 10-20 kDa. Active CPB was eliminated more slowly than proCPB and the activation peptide. Five percent of the activation peptide was detected nondegraded in the urine. After intraduodenal administration of the activation peptide there was no sign of the peptide in the urine.
Alternative usage of Otx2 promoters during mouse development

Our previous structural analysis of mouse Otx2 transcripts has revealed the existence of three different promoters and suggested that the corresponding mRNAs could exhibit specific expression patterns. Here, we analyze the precise dynamics of their expression throughout mouse development. Their spatial distribution was determined by isoform‐specific in situ hybridization and their relative abundance by real‐time reverse transcriptase‐polymerase chain reaction. Although the three promoters may be used in the same areas, we show that transcription preferentially occurs from the proximal promoter at onset of gene activity in early embryogenesis, and switches to the more distal one in most of the sites of expression in the adult brain. During gestation, their relative utilization becomes inverted. The third promoter, which shows no activity in embryonic stem cells and is moderately expressed during embryogenesis, is mostly used in specific areas derived from the rostral part of the neural tube. Developmental Dynamics 233:154–160, 2005. © 2005 Wiley‐Liss, Inc.
Exploring the Influence of Price and Convenience on Perceived Usefulness of On-line Banking within the TAM Framework: A Cross National (Canada and Spain) Decision Model

Nowadays, the Internet is a powerful mean to complement the traditional marketing channels used by banks. Based on the Technology Acceptance Model, this paper explores the importance of two external latent variables—‘Price’ and ‘Convenience’ —as antecedents of ‘Perceived Usefulness’ and consumer acceptance of on-line banking in a Canadian and Spanish environment; the results highlight the predictive power and accuracy of the model cross-nationally. In fact, the findings were quite similar in the Canadian and Spanish samples, and stress that ‘Perceived Usefulness’ and ‘Attitude’ are the key drivers of the consumers’ on-line banking acceptance. Conclusions and recommendations for future research are also provided.
Telomere Shortening Mechanisms

Telomeres are the terminal regions of the linear chromosomes of eukaryotes, which are composed of telomeric DNA and associated specific telomeric proteins. In most kinds of organisms, telomeric DNA is presented by a large number of repetitive, strictly defined short nucleotide sequences, such as: TTAGGG (in vertebrates), TTTAGGG (in the majority of terrestrial plants) and TTGGGG (in the ciliated infusoria Tetrahymena), etc. Although telomeric proteins differ among different groups of organisms they perform similar functions, which mainly consist of telomere length regulation and their protection against degradation (Grach, 2009). For a long time, it was considered that telomeres did not code RNA molecules and thus proteins. Subsequently, it was found that RNA is still transcribed from telomeres but that it did not encode any proteins. Further studies showed that this RNA plays an important role in telomere length regulation and chromatin reorganisation during both development and cell differentiation (Azzalin et al., 2007). In spite of the fact that telomeres do not code proteins, they also perform very important functions, the main role of which is to maintain the stability and functionality of the cellular genome. Among these are the protection of chromosomes from fusion with each other (Blackburn, 2001), participation in mitotic and meiotic chromosome segregation (Conrad et al., 1997; Dynek and Smith, 2004; Kirk et al., 1997), the stabilisation of broken chromosome ends (Pennaneach et al., 2006), their attachment to the nuclear envelope (Hediger et al., 2002; Podgornaya et al., 2000), influencing gene expression (Baur et al., 2001; Pedram et al., 2006), counting the quantity of cell divisions (Allsopp et al., 1992; Kurenova & Mason, 1997; Olovnikov, 1973), and also an original buffer function (Olovnikov, 1973). The latter consists of the protection of the mRNA coding regions of chromosomes from the end replication problem. The end replication problem consists of the impossibility of the full reproduction of the previous length of linear DNA ends on the leading telomeres during of the S-phase of the cell division cycle. It is caused by peculiarities in their structure and the functioning of the DNA replication machinery. As a result the telomeric regions of chromo‐
Dicer‐related drh‐3 gene functions in germ‐line development by maintenance of chromosomal integrity in Caenorhabditis elegans

In the course of systematic RNA interference (RNAi)‐based screens with helicase‐like genes in Caenorhabditis elegans, we have identified the drh‐3(D2005.5) gene as a candidate gene for protection against X‐ray irradiation. This gene encodes a novel RNA helicase‐like protein that is similar to two nematode Dicer‐related helicases (DRH). Here, we have showed the increased expression of drh‐3 transcripts during maturation of larvae to adults, and characterized the phenotype of drh‐3‐interferred nematodes using feeding RNAi method. RNAi‐mediated depletion of the drh‐3 transcripts caused embryonic lethality of F1 progeny and temperature‐sensitive reproductive capacity but did not affect the nematode life span. F1 progeny from drh‐3(RNAi) animals exhibited increased lethality after X‐ray irradiation or exposure to camptothecin. In drh‐3(RNAi) worms, aggregated chromosomes were observed in diakinesis oocyte nuclei. In developing early zygotic embryos from drh‐3(RNAi) worms, abnormally segregated chromosomes were observed and embryonic development was largely arrested at the mid‐stages of embryogenesis. Finally, examination of checkpoint responses in mitotic germ cells with regards to replication arrest by hydroxyurea and X‐ray‐induced DNA damage suggested that both checkpoints function normally under these genotoxic stress conditions. Taken together, these results indicate that the drh‐3 gene is essential for the development of germ‐lines by maintaining chromosomal integrity in C. elegans.
Performance of space-time codes for a large number of antennas

We study the asymptotic behavior of space-time codes when the number of transmit and receive antennas grows to infinity. Specifically, we determine the behavior of pairwise error probabilities with maximum-likelihood (ML) decoding and with three types of receiver interfaces: the ML interface, the linear zero-forcing (ZF) interface, and the linear minimum-mean-square-error (MMSE) interface. Two situations are studied: when the number of receiving antennas grows to infinity while the number of transmitting antennas is finite, and when both numbers grow to infinity but their ratio remains constant. We show that with ML or linear interfaces the asymptotic performance of space-time codes is determined by the Euclidean distances between codewords. Moreover, with the two linear interfaces examined here the number r of receive antennas must be much larger than the number t of transmit antennas to avoid a sizeable loss of performance; on the other hand, when r /spl Gt/ t, the performance of these linear interfaces comes close to that of ML. The dependence of error probabilities on Euclidean distance is valid for intermediate signal-to-noise ratios (SNRs) even when the number of antennas is small. Simulations validate our theoretical findings, and show how asymptotic results may be substantially valid even in a nonasymptotic regime: thus, even for few antennas, off-the-shelf codes may outperform space-time codes designed ad hoc.
Regional pest suppression associated with widespread Bt maize adoption benefits vegetable growers

Significance Area-wide Bacillus thuringiensis (Bt) adoption suppresses pests regionally, with declines expanding beyond the planted Bt crops into other non-Bt crop fields. The offsite benefits to vegetable crops from such pest suppression have not been documented. We show that widespread Bt field corn adoption is strongly associated with marked decreases in the number of recommended insecticidal applications, insecticides applied, and damage to vegetable crops in the United States. These positive impacts to growers, including organic producers, in the agricultural landscape expands on known ecological effects of Bt adoption. Transgenic crops containing the bacterium Bacillus thuringiensis (Bt) genes reduce pests and insecticide usage, promote biocontrol services, and economically benefit growers. Area-wide Bt adoption suppresses pests regionally, with declines expanding beyond the planted Bt crops into other non-Bt crop fields. However, the offsite benefits to growers of other crops from such regional suppression remain uncertain. With data spanning 1976–2016, we demonstrate that vegetable growers benefit via decreased crop damage and insecticide applications in relation to pest suppression in the Mid-Atlantic United States. We provide evidence for the regional suppression of Ostrinia nubilalis (Hübner), European corn borer, and Helicoverpa zea (Boddie), corn earworm, populations in association with widespread Bt maize adoption (1996–2016) and decreased economic levels for injury in vegetable crops [peppers (Capsicum annuum L.), green beans (Phaseolus vulgaris L.), and sweet corn (Zea mays L., convar. saccharata)] compared with the pre-Bt period (1976–1995). Moth populations of both species significantly declined in association with widespread Bt maize (field corn) adoption, even as increased temperatures buffered the population reduction. We show marked decreases in the number of recommended insecticidal applications, insecticides applied, and O. nubilalis damage in vegetable crops in association with widespread Bt maize adoption. These offsite benefits to vegetable growers in the agricultural landscape have not been previously documented, and the positive impacts identified here expand on the reported ecological effects of Bt adoption. Our results also underscore the need to account for offsite economic benefits of pest suppression, in addition to the direct economic benefits of Bt crops.
Honey bee protein atlas at organ-level resolution

Genome sequencing has provided us with gene lists but cannot tell us where and how their encoded products work together to support life. Complex organisms rely on differential expression of subsets of genes/proteins in organs and tissues, and, in concert, evolved to their present state as they function together to improve an organism's overall reproductive fitness. Proteomics studies of individual organs help us understand their basic functions, but this reductionist approach misses the larger context of the whole organism. This problem could be circumvented if all the organs in an organism were comprehensively studied by the same methodology and analyzed together. Using honey bees (Apis mellifera L.) as a model system, we report here an initial whole proteome of a complex organism, measuring 29 different organ/tissue types among the three honey bee castes: queen, drone, and worker. The data reveal that, e.g., workers have a heightened capacity to deal with environmental toxins and queens have a far more robust pheromone detection system than their nestmates. The data also suggest that workers altruistically sacrifice not only their own reproductive capacity but also their immune potential in favor of their queen. Finally, organ-level resolution of protein expression offers a systematic insight into how organs may have developed.
Neuropsychologic correlates of MRI white matter hyperintensities

To determine the effects of MRI white matter hyperintensities (WMH) on cognitive functioning, we used neuropsychologic tests and MRI to study 150 elderly volunteers free of neuropsychiatric or general disease. There were 76 (50.3%) individuals without and 74 (49.7%) with WMH. The latter subset was older (61.3 ± 6.6 years versus 58.5 ± 5.8 years, p = 0.0051, had a higher mean arterial blood pressure (103.7 ± 11.4 mm Hg versus 99.9 ± 10.3 mm Hg, p = 0.03), and a larger ventricular-to-intracranial-cavity ratio (6.3 ± 5.6% versus 4.7 ± 1.6%, p = 0.02). Individuals with WMH performed worse than their counterparts without such abnormalities on all tests administered. After adjusting for the group differences in age, arterial blood pressure, and ventricular size, we noted statistically significant results on form B of the Trail Making Test (121.8 ± 37.8 msec versus 100.3 ± 47.9 msec, p = 0.04), a complex reaction time task (680.8 ± 104.9 msec versus 607.1 ± 93.9 msec, p >= 0.001), and the assembly procedure of the Purdue Pegboard Test (27.5 ± 5.8 versus 30.6 ± 5.9, p = 0.02). Partial correlations did not reveal any relationship between test scores and the semiautomatically assessed total area of WMH. Our data suggest that the presence of WMH exerts a subtle effect on neuropsychologic performance of normal elderly individuals, which becomes particularly evident on tasks measuring the speed of more complex mental processing.