Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferring source attribution from a multiyear multisource data set of Salmonella in Minnesota

Salmonella enterica is a global health concern because of its widespread association with foodborne illness. Bayesian models have been developed to attribute the burden of human salmonellosis to specific sources with the ultimate objective of prioritizing intervention strategies. Important considerations of source attribution models include the evaluation of the quality of input data, assessment of whether attribution results logically reflect the data trends and identification of patterns within the data that might explain the detailed contribution of different sources to the disease burden. Here, more than 12,000 non‐typhoidal Salmonella isolates from human, bovine, porcine, chicken and turkey sources that originated in Minnesota were analysed. A modified Bayesian source attribution model (available in a dedicated R package), accounting for non‐sampled sources of infection, attributed 4,672 human cases to sources assessed here. Most (60%) cases were attributed to chicken, although there was a spike in cases attributed to a non‐sampled source in the second half of the study period. Molecular epidemiological analysis methods were used to supplement risk modelling, and a visual attribution application was developed to facilitate data exploration and comprehension of the large multiyear data set assessed here. A large amount of within‐source diversity and low similarity between sources was observed, and visual exploration of data provided clues into variations driving the attribution modelling results. Results from this pillared approach provided first attribution estimates for Salmonella in Minnesota and offer an understanding of current data gaps as well as key pathogen population features, such as serotype frequency, similarity and diversity across the sources. Results here will be used to inform policy and management strategies ultimately intended to prevent and control Salmonella infection in the state.
Pirfenidone reduces in vitro rat renal fibroblast activation and mitogenesis.

BACKGROUND Fibroblasts have been universally recognised in tubulointerstitial injury, where their presence has been shown to be a marker of disease progression. Recently, pirfenidone (PF) has been shown to both ameliorate progressive fibrosis and reduce established scarring after ureteric obstruction (UUO) in the rat, suggesting that it is a novel anti-fibrotic agent. The objective of this study was therefore to determine if these effects include down-regulation of fibroblast function. METHODS Cortical fibroblasts were obtained from outgrowth cultures of renal tissue isolated from kidneys 3 days after UUO and constituted 100% of cells studied. Functional studies examined the effects of 20 and 200 microg/ml PF on basal serum stimulated activity. Activation was examined by western blotting for alpha smooth muscle actin (alphaSMA) and connective tissue growth factor (CTGF). Cell proliferation, collagenase activity and collagen production were determined from kinetic studies, zymography for MMP2 and [3H] proline incorporation in collagenous proteins respectively. RESULTS Proliferation, as measured by [3H] thymidine incorporation, was reduced in dose dependent manner by 20 and 200 microg/ml PF (p<0.05; 200 vs 0 microg/ml). Likewise, 200 microg/ml PF reduced cell population growth over 5 days of culture (p<0.05 vs 0 microg/ml). PF (200 microg/ml) decreased alphaSMA and CTGF protein expression to 66+/-13 and 37+/-26% of basal levels respectively (both p<0.05 vs 0 microg/ml). Synthesis of collagen was unaffected by PF. Maximal dose of PF produced a modest reduction in MMP2 lytic activity (p=0.05). Effects of PF were independent of cell toxicity. CONCLUSIONS Down-regulation of renal fibroblast activation and proliferation are specific actions of PF.
HIRFL Water Level Monitoring System Research and Design

HIRFL system is the most advanced all-around heavy ion research facility. It is responsible for many of the scientific tasks in China, so to ensure its safe operation is a major responsibility by the Institute of Modern Physics, Chinese Academy of Science. There are many magnets and power needs water to cool, so the water system plays an important role in the whole HIRFL system. We design a set of water level monitoring system in order to protect the normal operation of the water system in this paper. It can monitoring tank level situation real-time, and visually displayed on a control room interface for water supply system of HIRFL. All of the design theory, and specific hardware and software design, and the specific operating results were given by this paper.
Working Paper Series Department of Economics Social Comparisons and Reference Group Formation : Some Experimental Evidence

We investigate reference group formation and the impact of social comparisons on ultimatum bargaining using a laboratory experiment. Three individuals compete in a real-e¤ort task for the role of the proposer in a three-player ultimatum game. The role of the responder is randomly allocated. The third individual receives a xed payment our treatment variable and makes no decision. The existence of a non-responder has a dramatic e¤ect on bargaining outcomes. In the most extreme treatment, more than half of the o¤ers are rejected. Behavior shows individuals exhibit self-serving bias in the way they de ne their reference groups. JEL Classi cation: C78, C91, D63
The development of the dendritic organization of primary and secondary motoneurons in the spinal cord of Xenopus laevis. An HRP study.

During embryonic and larval development of the clawed toad, Xenopus laevis, two different populations of motoneurons appear in the spinal cord. In this study the development of primary motoneurons which innervate the axial musculature (used during embryonic locomotion) and of secondary motoneurons which innervate the extremity musculature (used for locomotion during metamorphosis and thereafter) was analyzed with horseradish peroxidase (HRP) as a neuronal marker. After application of HRP to the axial musculature (rostral five postotic myotomes) the first labeled primary motoneurons were found at stage 24/25. During development gradually more labeled neurons were observed. These primary motoneurons send their dendrites into the marginal zone (white matter). At first only dorsal and lateral dendrites develop (stages 25-33), followed by ventral dendrites (stage 37/38). Up till stage 48 the developing dendrites extend throughout the marginal zone. Hereafter the marginal zone increases particularly at the dorsolateral edge, a development which is not followed by the dendrites of the primary motoneurons. The dendrites of mature primary motoneurons (stages 58-62) occupy the ventral and ventrolateral parts of the marginal zone. At stage 48, shortly after the hindlimb bud arises (stage 46, early metamorphosis), the first neurons related to this developing extremity could be labeled in the ventrolateral part of the lumbar spinal cord. At first these secondary motoneurons bear only a few dorsal dendrites of which only the tips reache out in the adjacent white matter. Already at stage 50 these dorsal dendrites have invaded the whole dorsolateral part of the marginal zone. Also the first ventral dendrites were observed at this stage. Later, at stage 53/54 also some ventral dendrites have reached the white matter together with a few lateral dendrites. At these early metamorphic stages already some primary afferent fibers were found making contact with the dorsomedial dendrites. At stage 58 for the first time recurrent axon collaterals were found, which extend into the ventromedial part of the marginal zone. The development of motoneurons in the spinal cord seems to be characterized by two phases: (1) establishment of contacts between motoneurons and target muscles, and (2) subsequent formation of connections of these motoneurons with other nerve cells within the central nervous system. The dendrites of primary motoneurons follow the development of the marginal zone, while dendrites of secondary motoneurons develop into an already well developed marginal zone. (ABSTRACT TRUNCATED AT 400 WORDS)
Plasmacytoid Dendritic Cells Regulate Breach of Self-Tolerance in Autoimmune Arthritis1

Achieving remission in rheumatoid arthritis (RA) remains elusive despite current biological therapeutics. Consequently, interest has increased in strategies to re-establish immune tolerance to provide long-term disease suppression. Although dendritic cells (DC) are prime candidates in initiating autoreactive T cell responses, and their presence within the synovial environment suggests a role in generation and maintenance of autoreactive, synovial T cell responses, their functional importance remains unclear. We investigated the contribution made by plasmacytoid DCs (pDCs) in the spontaneous breach of tolerance to arthritis-related self proteins, including rheumatoid factor, citrullinated peptide, and type II collagen observed in a novel arthritis model. Selective pDC depletion in vivo enhanced the severity of articular pathology and enhanced T and B cell autoimmune responses against type II collagen. pDC may offer a net anti-inflammatory function in the context of articular breach of tolerance. Such data will be vital in informing DC modulatory/therapeutic approaches.
Non-germ Line Restoration of Genomic Imprinting for a Small Subset of Imprinted Genes in Ubiquitin-like PHD and RING Finger Domain-Containing 1 (Uhrf1) Null Mouse Embryonic Stem Cells*

Background: Once erased, DNA methylation in imprinted genes was shown previously to be re-established only through germ line passage. Results: UHRF1 re-expression in Uhrf1−/− mouse embryonic stem (ES) cells restores DNA methylation for a few imprinted genes. Conclusion: DNA methylation in a few imprinted genes can be restored without germ line passage. Significance: ES cells can be a useful model for studying DNA methylation establishment in imprinted genes. The underlying mechanism for the establishment and maintenance of differential DNA methylation in imprinted genes is largely unknown. Previous studies using Dnmt1 knock-out embryonic stem (ES) cells demonstrated that, although re-expression of DNMT1 restored DNA methylation in the non-imprinted regions, the methylation patterns of imprinted genes could be restored only through germ line passage. Knock-out of Uhrf1, an accessory factor essential for DNMT1-mediated DNA methylation, in mouse ES cells also led to impaired global DNA methylation and loss of genomic imprinting. Here, we demonstrate that, although re-expression of UHRF1 in Uhrf1−/− ES cells restored DNA methylation for the bulk genome but not for most of the imprinted genes, it did rescue DNA methylation for the imprinted H19, Nnat, and Dlk1 genes. Analysis of histone modifications at the differential methylated regions of the imprinted genes by ChIP assays revealed that for the imprinted genes whose DNA methylation could be restored upon re-expression of UHRF1, the active histone markers (especially H3K4me3) were maintained at considerably low levels, and low levels were maintained even in Uhrf1−/− ES cells. In contrast, for the imprinted genes whose DNA methylation could not be restored upon UHRF1 re-expression, the active histone markers (especially H3K4me3) were relatively high and became even higher in Uhrf1−/− ES cells. Our study thus supports a role for histone modifications in determining the establishment of imprinting-related DNA methylation and demonstrates that mouse ES cells can be a valuable model for mechanistic study of the establishment and maintenance of differential DNA methylation in imprinted genes.
Self-supervised learning: When is fusion of the primary and secondary sensor cue useful?

Self-supervised learning (SSL) is a reliable learning mechanism in which a robot enhances its perceptual capabilities. Typically, in SSL a trusted, primary sensor cue provides supervised training data to a secondary sensor cue. In this article, a theoretical analysis is performed on the fusion of the primary and secondary cue in a minimal model of SSL. A proof is provided that determines the specific conditions under which it is favorable to perform fusion. In short, it is favorable when (i) the prior on the target value is strong or (ii) the secondary cue is sufficiently accurate. The theoretical findings are validated with computational experiments. Subsequently, a real-world case study is performed to investigate if fusion in SSL is also beneficial when assumptions of the minimal model are not met. In particular, a flying robot learns to map pressure measurements to sonar height measurements and then fuses the two, resulting in better height estimation. Fusion is also beneficial in the opposite case, when pressure is the primary cue. The analysis and results are encouraging to study SSL fusion also for other robots and sensors.
The Social Development Enterprise: The Case of Public Services in Latin America

The general basis of this proposal is that the organization that we will call a “social development enterprise” is what best provides the public services of water and sanitation. The first contention (or differing characteristic and typifying condition) is that the objectives of the organization are integrated with those of society. Thus they are services and are public (for the entire population). The moral and social basis on which society allows and promotes the existence of organizations, delegating to them the monopoly of service, is that they should exist for the well-being of that society. Given the importance of the water infrastructure for the very subsistence of society, the correct functioning of this model (the integration of the objectives of the organization with those of society) is crucial, just as it must function as a monopoly (that is that the traditional rules of the market do not apply, for this model is another aspect of the social development enterprise). To act differently to this, within an alternative framework, will guarantee such tensions that in the long run the developing situation will lead to the exclusion of such organization, which will be seen as an obstacle to development. That is a big frustration.From the neo-ideological or publicists’ perspective the nature of these organizations is important, that is, are they state-run or private? In our proposal this difference is not significant; on the contrary, it is a central plank of the proposal to define what the role of the private sector should be in these organizations. Should it be the habitual and comfortable role of contractor, concession holder or owner, or rather should the private sector be a responsible participant in the social development enterprise? The role of the private sector in these organizations being defined, the model integrating public sector services (which may be extended to other public services) into society may be developed. The commitment to efficient management with appropriate checks and above all, transparency will be sufficient to successfully satisfy the social demand for development - a pending matter that is no longer postponable.
Apheresis‐related enrichment of CD26++ T lymphocytes: phenotypic characterization and correlation with unfavorable outcome in autologous hematopoietic progenitor cell transplantation

BACKGROUND: The lymphocyte surface glycoprotein CD26 anchors adenosine deaminase to the lymphocyte surface and possesses dipeptidyl peptidase IV activity. A distinct subset of CD26++ lymphocytes in autologous hematopoietic progenitor cell transplants (HPCTs) was investigated with regard to clinical outcome after autologous HPCT. The phenotype of these cells was characterized in more detail.
Microtubules Are required for motility and positioning of vesicles and mitochondria in hyphal tip cells of Allomyces macrogynus.

We have used video-enhanced light microscopy and digital image processing to characterize the intracellular motility and positioning of vesicles ( approximately 1-microm diameter) and mitochondria in growing hyphal tip cells of Allomyces macrogynus. These observations were coupled with cytoskeletal inhibitory experiments to define the roles of the microtubule and actin cytoskeletons in organelle translocation and positioning. Vesicles and mitochondria were abundant in apical and subapical hypha regions. Vesicles traveled along paths that were parallel to the longitudinal axis of the cell. Anterograde (i.e., toward the hyphal apex) and retrograde (i.e., away from the hyphal apex) movements of vesicles occurred at average rates of 4.0 and 2.2 microm/s, respectively. Bidirectional travel of vesicles along common paths was noted in the cortical cytoplasm. Mitochondria were aligned mostly parallel to the long axis of the hypha, except those extending into the hyphal apex, which were oriented toward the Spitzenkörper. In regions of the subapical hypha mitochondria were often restricted to the cortical cytoplasm and nuclei occupied the central cytoplasmic region. Mitochondria displayed rapid anterograde movements reaching speeds of 3.0 microm/s, but primarily maintained a constant position relative to either the advancing cytoplasm or the lateral cell wall. Cytoskeletal disruption experiments showed that the positioning of mitochondria and motility of vesicles and mitochondria were microtubule-based and suggested that the actin cytoskeleton played uncertain roles.
Rapid Identification and Typing ofStaphylococcus aureus by PCR-Restriction Fragment Length Polymorphism Analysis of the aroA Gene

ABSTRACT The Staphylococcus aureus aroA gene, which encodes 5-enolpyruvylshikimate-3-phosphate synthase, was used as a target for the amplification of a 1,153-bp DNA fragment by PCR with a pair of primers of 24 and 19 nucleotides. The PCR products, which were detected by agarose gel electrophoresis, were amplified from all S. aureus strains so far analyzed (reference strains and isolates from cows and sheep with mastitis, as well as 59 isolates from humans involved in four confirmed outbreaks). Hybridization with an internal 536-bp DNA fragment probe was positive for all PCR-positive samples. No PCR products were amplified when other Staphylococcus spp. or genera were analyzed by using the same pair of primers. The detection limit for S. aureus cells was 20 CFU when the cells were suspended in saline; however, the sensitivity of the PCR was lower (5 × 102 CFU) when S. aureus cells were suspended in sterilized whole milk. TaqI digestion of the PCR-generated products rendered two different restriction fragment length polymorphism patterns with the cow and sheep strains tested, and these patterns corresponded to the two different patterns obtained by antibiotic susceptibility tests. Analysis of the 59 human isolates by our easy and rapid protocol rendered results similar to those of other assays.
CodY orchestrates the expression of virulence determinants in emetic Bacillus cereus by impacting key regulatory circuits

Bacillus cereus causes gastrointestinal diseases and local and systemic infections elicited by the depsipeptide cereulide, enterotoxins, phospholipases, cytolysins and proteases. The PlcR‐PapR quorum sensing system activates the expression of several virulence factors, whereas the Spo0A‐AbrB regulatory circuit partially controls the plasmid‐borne cereulide synthetase (ces) operon. Here, we show that CodY, a nutrient‐responsive regulator of Gram‐positive bacteria, has a profound effect on both regulatory systems, which have been assumed to operate independently of each other. Deletion of codY resulted in downregulation of virulence genes belonging to the PlcR regulon and a concomitant upregulation of the ces genes. CodY was found to be a repressor of the ces operon, but did not interact with the promoter regions of PlcR‐dependent virulence genes in vitro, suggesting an indirect regulation of the latter. Furthermore, CodY binds to the promoter of the immune inhibitor metalloprotease InhA1, demonstrating that CodY directly links B. cereus metabolism to virulence. In vivo studies using a Galleria mellonella infection model, showed that the codY mutant was substantially attenuated, highlighting the importance of CodY as a key regulator of pathogenicity. Our results demonstrate that CodY profoundly modulates the virulence of B. cereus, possibly controlling the development of pathogenic traits in suitable host environments.
II. Yeast sequencing reports. The sequence of a 22·4 kb DNA fragment from the left arm of yeast chromosome II reveals homologues to bacterial proline synthetase and murine α‐adaptin, as well as a new permease and a DNA‐binding protein

We report the sequencing of a 22 470 bp DNA fragment from the left arm of Saccharomyces cerevisiae chromosome II. Thirteen open reading frames longer than 300 bp provisionally called YBL0520, YBL0401 to YBL0408 and YBL0410 to YBL0413 have been detected. Five genes were previously sequenced: COR1, encoding a core protein of the mitochondrial coenzyme QH2 cytochrome c reductase complex (Tzagaloff and Crivellone, 1986). PRS3, a proteasome subunit gene (Lee et al., 1992), ERD2, coding for a protein involved in the secretory pathway (Semeza et al., 1990), URA7, which encodes a CTP synthetase (Ozier‐Kalogeropoulos et al., 1991) and the gene for the ribosomal protein L16 (Pan et al., 1993). Among the others, YBL0406 shows striking homologies to FUR4 (Jund et al., 1988) and DAL4 (Yoo et al., 1992), the uracyl and allantoin permeases; YBL0520 is a DNA‐related protein, possibly involved in gene regulation; YBL0412 shares homologies with the mouse α‐adaptins A and C; and YBL0413 is homologous to a protein of Pseudomonas aeruginosa that is likely to be involved in proline biosynthesis. YBL0401, internal to YBL0520, is probably not expressed. The sequence has been deposited in the EMBL data library under accession number X78217
One-Lung Ventilation with Additional Ipsilateral Ventilation of Low Tidal Volume and High Frequency in Lung Lobectomy

Background To investigate the protective effects of additional ipsilateral ventilation of low tidal volume and high frequency on lung functions in the patients receiving lobectomy. Material/Methods Sixty patients receiving lung lobectomy were randomized into the conventional one-lung ventilation (CV) group (n=30) and the ipsilateral low tidal volume high frequency ventilation (LV) group (n=30). In the CV group, patients received only contralateral OLV. In the LV group, patients received contralateral ventilation and additional ipsilateral ventilation of low tidal volume of 1–2 ml/kg and high frequency of 40 times/min. Normal lung tissues were biopsied for the analysis of lung injury. Lung injury was scored by evaluating interstitial edema, alveolar edema, neutrophil infiltration, and alveolar congestion. Results At 30 min and 60 min after the initiation of one-lung ventilation and after surgery, patients in the LV group showed significantly higher ratio of the partial pressure of arterial oxygen to the fraction of inspired oxygen than those in the CV group (P<0.001). Lung injury was significantly less severe (2.7±0.7) in the LV group than in the CV group (3.1±0.7) (P=0.006). Conclusions Additional ipsilateral ventilation of low tidal volume and high frequency can decrease the risk of hypoxemia and alleviate lung injury in patients receiving lobectomy.