Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmid required for virulence of Agrobacterium tumefaciens

The irreversible loss of crown gall-inducing ability of Agrobacterium tumefaciens strain C-58 during growth at 37 C is shown to be due to loss of a large plasmid (1.2 X 10-8 daltons). The gene responsible for this high rate of plasmid loss at elevated temperatures seems to be located on the plasmid. In addition, another spontaneous avirulent variant, A. tumefaciens strain IIBNV6 is shown to lack the virulence plasmid which its virulent sibling strain, IIBV7, possesses. Deoxyribonucleic acid reassociation measurements prove that the plasmid is eliminated, not integrated into the chromosome, in both of the avirulent derivatives. Transfer of virulence from donor strain C-58 to avirulent recipient strain A136 results from the transfer of a plasmid, which appears identical to the donor plasmid by deoxyribonucleic acid reassociation measurements. The transfer of virulence in another cross, K27 X A136, was also shown to result from the transfer of a large plasmid. These findings establish unequivocally that the large plasmid determines virulence. Two additional genetic determinants have been located on the virulence plasmid of A. tumefaciens strain C-58: the ability to utilize nopaline and sensitivity to a bacteriocin produced by strain 84. The latter trait can be exploited for selection of avirulent plasmid-free derivatives of strain C-58. The trait of nopaline utilization appears to be on the virulence plasmid also in strains IIBV7 and K27.
Measurement of glutathione S‐transferase P1‐1 in plasma

Gastrointestinal tumors often contain high amounts of the detoxification enzyme glutathione S‐transferase P1‐1 (GSTP1‐1). Elevated levels of GSTP1‐1 were found in serum and plasma from most patients with gastrointestinal tumors. The authors evaluated the role of GSTP1‐1 as a plasma tumor marker in patients with gastrointestinal tumors.
Non-parametric feature selection for machine learning in complex settings

In our big data society, the possibilities of acquiring and storing data are continuously increasing. Therefore, very large datasets are often constructed for a given prediction problem. Besides a large number of data points, these datasets often also contain lots of features, corresponding to the characteristics measured for each data point. Lacking of prior information about the relevance of the collected features, practionners often consider the whole available information; they thus have to deal with databases containing a huge number of features, while many of them are generally redundant or irrelevant for the considered problem. The task of feature selection consists in detecting a small set of features which are relevant and informative for the considered problem. Feature selection is often recognized as a preprocessing step of major importance, resulting in many potential benefits. These include improving the performances of prediction models and speeding up their construction, reducing the data acquisition and storage costs as well as better understanding and more easily interpreting the problems at hand. Because of the aforementioned motivations, feature selection has become an extremely active reasearch field. However, most existing works are dedicated to classical prediction problems, where a complete dataset of continuous or categorical features and a full output target vector are available. Nevertheless, in many situtations, data is not encountered in such an ideal form. The main objective of the thesis is therefore to propose efficient feature selection algorithms for non-standard situations, that we generically denote as complex settings. More precisely, four kinds of problems are tackled in the thesis : semi-supervised problems, multi-label classification, datasets with missing values and problems with uncertain/noisy labels. All these settings correspond to frequently encountered problems, which are important to address in practice. The second objective of this thesis is more theoretical. We study the adequacy of the mutual information as a feature selection criterion, regarding the Bayes risk for classification problems and the mean squared and the mean absolute error for regression problems. This study gives valuable insights on the behaviour of the mutual information for feature selection.
Morphological Features of the Apical Region in the Principal Cells of Mongrel Dog Epididymis

Las celulas epiteliales principales son el tipo de celula que predominan en el epididimo. Estas celulas han demostrado ser secretoras y endociticas. La region apical del citoplasma de las celulas principales en el perro Mongrel, se encuentran muy cerca del apice celular y lumen tubular, mostrando microvellosidades en el limite luminal y un aparato endocitico, el que consiste en depresiones recubiertas y vesiculas, endosomas de diversos tamanos, cuerpos multivesiculares y lisosomas. Los endosomas, cuerpos multivesiculares y lisosomas contienen granulos electrodensos. Estos resultados sugieren que las celulas principales del epididimo, en el perro, poseen un aparato endocitico altamente desarrollado que juega un importante rol en la endocitosis. Estas celulas funcionan de manera similar a la correspondiente en otros mamiferos, en el desempeno de endocitosis.
Decreased CD4+CD25+bright T cells in peripheral blood of patients with primary Sjögren's syndrome

CD4+CD25 +bright T cells played a crucial role in the suppression of immune response. Recently, decreased levels of CD4+CD25+bright T cells in the peripheral blood of patients with systemic lupus erythematosus were reported, suggesting the potential role of CD4+CD25+bright T cells in human autoimmune diseases. Primary Sjögren's syndrome (pSS) is another common human systemic autoimmune disease. The present study aimed to investigate the levels of CD4+CD25+bright T cells in pSS and to correlate their levels with some biomarkers of inflammation and immune activation. Thirty-three patients with pSS and 35 age- and sex-matched normal individuals were enrolled in the study. The flowcytometric method was applied in the measurement of CD4+CD25+bright T cells. The results showed that patients with pSS had statistically lower levels of CD4+CD25+bright T cells than normal controls, expressed either as absolute cell numbers (mean ± SD: 47.07 ± 25.53 cells/mm 3 versus 79.55 ± 34.56 cells/mm3, P < 0.001) or as percentages of peripheral blood mononuclear cells (mean ± SD: 2.79 ± 1.06% versus 3.84 ± 1.42%, P < 0.001) or as percentages of CD4+ T cells (mean ± SD: 7.85 ± 2.62% versus 11.68 ± 3.78%, P < 0.005). Moreover, there were statistically significant inverse correlations between the levels of CD4+CD25+bright T cells and some parameters of inflammation or immune activation including erythrocyte sedimentation rate, C-reactive protein, IgG and rheumatoid factors. The result suggested that CD4+CD25+bright T cells were likely to play anti-inflammatory and immunosuppressive roles in the pathogenesis of pSS. However, the exact functions of decreased circulating CD4+CD25+bright T cells in pSS need further elucidated. Lupus (2008) 17, 34—39.
High-speed gallop locomotion in the Thoroughbred racehorse. I. The effect of incline on stride parameters

SUMMARY During locomotion up an incline, power is required to elevate the centre of mass. This is provided when the animal's limbs are in contact with the ground. Measurements of stride timing variables from multiple limbs during high speed, over-ground locomotion would enhance our understanding of locomotor powering during changes in terrain. This study measured foot-on and foot-off times from galloping horses using a previously validated system of limb-mounted accelerometers and a global positioning system data logger. A detailed track survey provided incline information from all areas of the track. Measurements were made from six horses over a speed range of 9 to 13 m s–1. Foot-fall timings were used to calculate variables, which included stance duration, protraction duration, stride frequency and duty factor. The relationship between track incline and measured variables was assessed. Stride variables from horses galloping on level (0–2% incline) and incline (8–12% incline) sections of the track were compared. Fore- and hindlimb protraction durations were significantly reduced across the speed range during incline galloping (P=0.001). This resulted in a mean increase in stride frequency from 2.01 to 2.08 strides s–1 at 9.5 m s–1 and 2.10 to 2.17 strides s–1 at 12.5 m s–1 during incline galloping. Duty factor was significantly greater for the hindlimbs during incline galloping (P<0.001), increasing from 0.31 to 0.32 at 9.5 m s–1 and 0.28 to 0.29 at 12.5 m s–1. Peak limb force was calculated from duty factor and assumed fore- to hindlimb impulse distributions. Smaller peak vertical forces were calculated in the forelimbs and increased peak vertical forces were calculated in the hindlimbs when galloping on an incline. Measured changes in stride timing variables differ from those reported in trotting horses. We propose that horses increase their stride frequency at a given speed during incline galloping to provide power for moving the centre of mass up the slope.
Assimilation and attachment in the context of international migration: the case of guestworkers in Germany.

"Immigrants' attachments to home and their assimilation into the host society have been identified as major factors influencing international return migration. This paper provides an empirical analysis of the determinants of attachment and assimilation, with a special focus on the impact of duration of stay. Using survey data on guestworkers in West Germany in 1984 and 1989, the study finds that assimilation increases at a decreasing rate as the duration of stay is extended. The relationship between attachment and length of stay is less strong, but shows a general trend of decreasing attachment levels as guestworkers prolong their stay in Germany. The resulting trends for return migration are characterized by an overall decline in the propensity to return as the duration of stay is extended. However, the rate of decline varies by gender, marital status, and nationality. Overall, the results allude to the importance of distinguishing between short term and long term immigrants. "
HOST‐TUMOR ANTAGONISM. XII. POSSIBLE EFFECT OF THE CORTISONE DRUGS ON THE DEVELOPMENT OF METASTASES IN PATIENTS WITH CARCINOMA †

Several cases of carcinoma have come to our attention in which it was felt that administration of cortisone or its derivatives for treatment of another ailment was associated with the development of metastases. This hypothesis cannot be proved in the human subject, since we do not know why cancers metastasize; all that can be said is that the development of metastases coincided in time with the use of the cortisone drugs. Others have noted this coincidence. For example, a report of the meeting of the Sub-committee on Steroids and Cancer which appeared in the Journal of the American Medical Association (1) contains the following statement: "Cortisone and ACTH have been tested in terminal cases of various types of neoplasia. These agents allay pain and induce a sense of well-being, but do not alter the course of the disease. In several cases, despite the subjective response and the improved general condition of the patient, there was evidence of more rapid spread of the neoplasm, and autopsy later even revealed that the spleen had been riddled with metastases. " In an article by Shimkin and Moore (2), the statement appears, "Many investigators have noted that cortisone reduces host resistance, with resultant acceleration of tumor implantation and growth. " This latter statement refers to work in experimental animals and is extremely well documented. It is the purpose of this article 1) to review the animal work describing the effect of cortisone on the implanted tumor and the development of metastases, 2) to describe the possible ways in which metastases may be produced, and 3) to describe several patients in which the development of metastases coincided in time with the use of cortisone drugs.
Origins of knowledge and innovation in R&D alliances: a contingency approach

Innovative performance is influenced both by the origins of the existing knowledge that is combined to generate innovation and by how economic actors search for new knowledge. Drawing on a sample of inter-firm dyadic R&D alliances, we found that whereas the integration of geographically distant knowledge and of organisationally proximate knowledge in R&D alliances are negatively related to the alliance innovative performance, search span positively moderates both relationships. We conclude that, in order to make the most of broad-span searching, firms participating in R&D alliances should integrate geographically distant but organisationally proximate knowledge. By doing so, firms take advantage of the diversity and novelty that characterises geographically distant knowledge, while preserving considerable levels of relative absorptive capacity that are needed for them to understand, internalise, and effectively use partners’ knowledge from different domains.
M‐sec regulates polarized secretion of inflammatory endothelial chemokines and facilitates CCL2‐mediated lymphocyte transendothelial migration

Activation of endothelial cells by IL‐1β triggers the expression of multiple inflammatory cytokines and leukocyte‐attracting chemokines. The machineries involved in the secretion of these inducible proteins are poorly understood. With the use of genome‐wide transcriptional analysis of inflamed human dermal microvascular endothelial cells, we identified several IL‐1β−induced candidate regulators of these machineries and chose to focus our study on TNF‐α‐induced protein 2 (myeloid‐secretory). The silencing of myeloid‐secretory did not affect the ability of inflamed endothelial cells to support the adhesion and crawling of effector T lymphocytes. However, the ability of these lymphocytes to complete transendothelial migration across myeloid‐secretory‐silenced human dermal microvascular endothelial cells was inhibited significantly. These observed effects on lymphocyte transendothelial migration were recovered completely when exogenous promigratory chemokine CXCL12 was overlaid on the endothelial barrier. A polarized secretion assay suggested that the silencing of endothelial myeloid‐secretory impairs T effector transendothelial migration by reducing the preferential secretion of endothelial‐produced CCL2, a key transendothelial migration‐promoting chemokine for these lymphocytes, into the basolateral endothelial compartment. Myeloid‐secretory silencing also impaired the preferential secretion of other endothelial‐produced inflammatory chemokines, as well as cytokines, such as IL‐6 and GM‐CSF, into the basolateral endothelial compartment. This is the first evidence of a novel inflammation‐inducible machinery that regulates polarized secretion of endothelial CCL2 and other inflammatory chemokines and cytokines into basolateral endothelial compartments and facilitates the ability of endothelial CCL2 to promote T cell transendothelial migration.
Associations of Calcium and Milk Product Intakes with Incident, Sporadic Colorectal Adenomas

ABSTRACT Calcium intake has been consistently, modestly inversely associated with colorectal neoplasms, and supplemental calcium reduced adenoma recurrence in clinical trials. Milk products are the major source of dietary calcium in the United States, but their associations with colorectal neoplasms are unclear. Data pooled from three colonoscopy-based case-control studies of incident, sporadic colorectal adenoma (n = 807 cases, 2,185 controls) were analyzed using multivariable unconditional logistic regression. Residuals from linear regression models of milk with dietary calcium were estimated as the noncalcium, insulin-like growth factor 1-containing component of milk. For total, dietary, and supplemental calcium intakes, the adjusted odds ratios (ORs) comparing the highest to the lowest intake quintiles were 0.94 (95% confidence interval [CI] 0.69–1.30), 0.86 (CI 0.62–1.20), and 0.99 (CI 0.77–1.27), respectively. The corresponding ORs for consumption of total milk products, total milk, nonfat milk, total milk product residuals, and nonfat milk residuals were, respectively, 0.99, 0.90, 0.92, 0.94, and 0.95; all CIs included 1.0. For those who consumed any whole milk relative to those who consumed none, the OR was 1.15 (CI 0.89–1.49). These results are consistent with previous findings of modest inverse associations of calcium intakes with colorectal adenoma, but suggest that milk products may not be associated with adenoma.
Alternative exon definition events control the choice between nuclear retention and cytoplasmic export of U11/U12-65K mRNA

Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3′ untranslated region (3′UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3′UTR to non-productive isoforms with a long 3′UTR that are retained in the nucleus or/and spliced to the downstream amylase locus. Importantly, the choice between these alternatives is determined by alternative terminal exon definition events regulated by conserved U12- and U2-type 5′ splice sites as well as sequence signals used for pre-mRNA cleavage and polyadenylation. We additionally show that U11 snRNP binding to the U11/U12-65K mRNA species with a long 3′UTR is required for their nuclear retention. Together, our studies uncover an intricate molecular circuitry regulating the abundance of a key spliceosomal protein and shed new light on the mechanisms limiting the export of non-productively spliced mRNAs from the nucleus to the cytoplasm.
The influence of age on colonic epithelial cell proliferation

Cancer of the large bowel is relatively rare in persons younger than 50 years of age, but its incidence increases sharply in persons older than 60 years of age. We thought that the evaluation of colonic cell proliferation, an accurate biomarker of predisposition to colorectal cancer, might help to elucidate the susceptibility of elderly persons to this common malignancy. Accordingly, 30 persons with normal lower endoscopy results were divided into three age groups (30 to 50,51 to 65, and 66 to 90 years of age; Groups 1, 2, and 3, respectively). Samples of rectal mucosa were taken at endoscopic examination, incubated with [3H]thymidine, and processed with standard autoradiographic techniques. At histologic examination, each intestinal hemicrypt was divided into five equal longitudinal compartments from the fundus (compartment 1) to the surface (compartment 5). The number and the position of labeled cells along the crypt were recorded. The total labeling index (LI) (the ratio of labeled cells to total cells) was significantly higher in Group 3 than in the two other groups. Similarly, the LI per crypt compartment in the most superficial portions of the crypts was consistently higher in persons older than 65 years of age (P < 0.01 at least), indicating an expansion of the proliferative zone to the most superficial portion of the colonic glands. When the proliferative profiles of the three groups of subjects investigated were compared with those of patients with polyps, an almost complete overlap of values was observed between this population at increased risk for cancer and the subjects in Group 3. We conclude that aging is characterized by an overall increase of epithelial cell proliferation in colorectal mucosa and by an upwards expansion of the proliferative compartment, similar to that observed in a population at risk for cancer of the large bowel.
ANTIBODY RESPONSE TO VACCINES FOR RHINOTRACHEITIS, CALICIVIRAL DISEASE, PANLEUKOPENIA, FELINE LEUKEMIA, AND RABIES IN TIGERS (PANTHERA TIGRIS) AND LIONS (PANTHERA LEO)

Abstract: This article presents the results of a study of captive tigers (Panthera tigris) and lions (Panthera leo) vaccinated with a recombinant vaccine against feline leukemia virus; an inactivated adjuvanted vaccine against rabies virus; and a multivalent modified live vaccine against feline herpesvirus, calicivirus, and panleukopenia virus. The aim of the study was to assess the immune response and safety of the vaccines and to compare the effects of the administration of single (1 ml) and double (2 ml) doses. The animals were separated into two groups and received either single or double doses of vaccines, followed by blood collection for serologic response for 400 days. No serious adverse event was observed, with the exception of abortion in one lioness, potentially caused by the incorrect use of the feline panleukopenia virus modified live vaccine. There was no significant difference between single and double doses for all vaccines. The recombinant vaccine against feline leukemia virus did not induce any serologic response. The vaccines against rabies and feline herpesvirus induced a significant immune response in the tigers and lions. The vaccine against calicivirus did not induce a significant increase in antibody titers in either tigers or lions. The vaccine against feline panleukopenia virus induced a significant immune response in tigers but not in lions. This report demonstrates the value of antibody titer determination after vaccination of nondomestic felids.
Automated Disambiguation of Acronyms and Abbreviations in Clinical Texts: Window and Training Size Considerations

Acronyms and abbreviations within electronic clinical texts are widespread and often associated with multiple senses. Automated acronym sense disambiguation (WSD), a task of assigning the context-appropriate sense to ambiguous clinical acronyms and abbreviations, represents an active problem for medical natural language processing (NLP) systems. In this paper, fifty clinical acronyms and abbreviations with 500 samples each were studied using supervised machine-learning techniques (Support Vector Machines (SVM), Naïve Bayes (NB), and Decision Trees (DT)) to optimize the window size and orientation and determine the minimum training sample size needed for optimal performance. Our analysis of window size and orientation showed best performance using a larger left-sided and smaller right-sided window. To achieve an accuracy of over 90%, the minimum required training sample size was approximately 125 samples for SVM classifiers with inverted cross-validation. These findings support future work in clinical acronym and abbreviation WSD and require validation with other clinical texts.
Glutamine Involvement in Nitrogen Control of Gibberellic Acid Production in Gibberella fujikuroi

When the fungus Gibberella fujikuroi ATCC 12616 was grown in fermentor cultures, both intracellular kaurene biosynthetic activities and extracellular GA3 accumulation reached high levels when exogenous nitrogen was depleted in the culture. Similar patterns were exhibited by several nonrelated enzymatic activities, such as formamidase and urease, suggesting that all are subject to nitrogen regulation. The behavior of the enzymes involved in nitrogen assimilation (glutamine synthetase, glutamate dehydrogenase, and glutamate synthase) during fungal growth in different nitrogen sources suggests that glutamine is the final product of nitrogen assimilation in G. fujikuroi. When ammonium or glutamine was added to hormone-producing cultures, extracellular GA3 did not accumulate. However, when the conversion of ammonium into glutamine was inhibited by L-methionine-DL-sulfoximine, only glutamine maintained this effect. These results suggest that glutamine may well be the metabolite effector in nitrogen repression of GA3 synthesis, as well as in other nonrelated enzymatic activities in G. fujikuroi.