Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of foods in sporadic listeriosis. II. Microbiologic and epidemiologic investigation. The Listeria Study Group.

OBJECTIVE To evaluate the role of foods in sporadic listeriosis. DESIGN Microbiologic survey of foods collected from refrigerators of patients with listeriosis identified through active laboratory-based surveillance. Patient and food Listeria monocytogenes isolates were subtyped to identify foods contaminated with the same strain of L monocytogenes that caused illness in the patient; samples of these foods were obtained from the retail source. SETTING Multistate population-based study conducted between 1988 and 1990. RESULTS Listeria monocytogenes grew from at least one food specimen in the refrigerators of 79 (64%) of 123 listeriosis patients; 11% of more than 2000 food specimens collected in the study contained L monocytogenes. Twenty-six (33%) of 79 refrigerators with foods that grew L monocytogenes contained at least one food isolate of the same strain as that in the corresponding patient, a frequency much higher than would be expected by chance (P less than .001). Multivariate analysis showed that of the food specimens that grew L monocytogenes, foods that were ready-to-eat, foods that grew L monocytogenes by a direct-plating method (a measure of the level of contamination), and foods that contained serotype 4b isolates were independently associated with an increased likelihood of containing the patient-matching strain. CONCLUSION We identified specific food and L monocytogenes isolate characteristics--ready-to-eat foods, foods containing higher concentrations of L monocytogenes, and foods containing serotype 4b--which were associated with disease-causing strains. These results can provide guidance to industry and regulatory agencies in developing strategies to prevent listeriosis.
Supervised learning technique for the automated identification of white matter hyperintensities in traumatic brain injury

Abstract Background: White matter hyperintensities (WMHs) are foci of abnormal signal intensity in white matter regions seen with magnetic resonance imaging (MRI). WMHs are associated with normal ageing and have shown prognostic value in neurological conditions such as traumatic brain injury (TBI). The impracticality of manually quantifying these lesions limits their clinical utility and motivates the utilization of machine learning techniques for automated segmentation workflows. Methods: This study develops a concatenated random forest framework with image features for segmenting WMHs in a TBI cohort. The framework is built upon the Advanced Normalization Tools (ANTs) and ANTsR toolkits. MR (3D FLAIR, T2- and T1-weighted) images from 24 service members and veterans scanned in the Chronic Effects of Neurotrauma Consortium’s (CENC) observational study were acquired. Manual annotations were employed for both training and evaluation using a leave-one-out strategy. Performance measures include sensitivity, positive predictive value, score and relative volume difference. Results: Final average results were: sensitivity = 0.68 ± 0.38, positive predictive value = 0.51 ± 0.40, = 0.52 ± 0.36, relative volume difference = 43 ± 26%. In addition, three lesion size ranges are selected to illustrate the variation in performance with lesion size. Conclusion: Paired with correlative outcome data, supervised learning methods may allow for identification of imaging features predictive of diagnosis and prognosis in individual TBI patients.
Disassociation between the effects of amino acids and insulin on signaling, ubiquitin ligases, and protein turnover in human muscle

We determined the effects of intravenous infusion of amino acids (AA) at serum insulin of 5, 30, 72, and 167 mU/l on anabolic signaling, expression of ubiquitin-proteasome components, and protein turnover in muscles of healthy young men. Tripling AA availability at 5 mU/l insulin doubled incorporation of [1-13C]leucine [i.e., muscle protein synthesis (MPS), P < 0.01] without affecting the rate of leg protein breakdown (LPB; appearance of d5-phenylalanine). While keeping AA availability constant, increasing insulin to 30 mU/l halved LPB (P < 0.05) without further inhibition at higher doses, whereas rates of MPS were identical to that at 5 mU/l insulin. The phosphorylation of PKB Ser473 and p70S6k Thr389 increased concomitantly with insulin, but whereas raising insulin to 30 mU/l increased the phosphorylation of mTOR Ser2448, 4E-BP1 Thr37/46, or GSK3β Ser9 and decreased that of eEF2 Thr56, higher insulin doses to 72 and 167 mU/l did not augment these latter responses. MAFbx and proteasome C2 subunit proteins declined as insulin increased, with MuRF-1 expression largely unchanged. Thus increasing AA and insulin availability causes changes in anabolic signaling and amounts of enzymes of the ubiquitin-proteasome pathway, which cannot be easily reconciled with observed effects on MPS or LPB.
AHTM: Achieving efficient flow table utilization in Software Defined Networks

In Software Defined Networks (SDN), more packet fields are included to design fine-grained policies. These policies are stored as entries in switch Flow Table. However, fine-grained policies cause the scalability issue as a single flow entry needs larger storage space and a significant number of flow entries need to be stored, but the Flow Table is limited due to the constraints of Ternary Content Addressable Memory (TCAM). To address this issue, we propose Adaptive Hard Timeout Method (AHTM) to improve the Flow Table utilization by optimizing the timeouts of flow entries, thus the Flow Table is reused efficiently. AHTM models the Flow Table as a queueing system and derives closed-form formulas for analysis and optimization. We also implement AHTM as a light-weighted SDN application and it offers interfaces to other applications. The simulation results show that AHTM can achieve the balance between blocking probability and extra workload to SDN controller.
Managing resource and technology interdependencies in project portfolio: A case-study results

In multi-project management, projects can not be taken in isolated way. They have often interdependencies with each-other, such as sharing human resources and modularized structure, and knowledge diffusion. Managing these relationships in portfolio selection and review process helps to make more effective selection choices and increase projects success rate in project portfolio management. There are many methods available to support interdependency management, but recent empirical findings show that not many of them are used in practice. In the present research, a multiple case study was performed to find out how interdependencies are managed in real life. The results show that interdependencies are mostly managed by informal ways. A description of managing interdependencies is given.
Golgi-Mediated Synthesis and Secretion of Matrix Polysaccharides of the Primary Cell Wall of Higher Plants

The Golgi apparatus of eukaryotic cells is known for its central role in the processing, sorting, and transport of proteins to intra- and extra-cellular compartments. In plants, it has the additional task of assembling and exporting the non-cellulosic polysaccharides of the cell wall matrix including pectin and hemicelluloses, which are important for plant development and protection. In this review, we focus on the biosynthesis of complex polysaccharides of the primary cell wall of eudicotyledonous plants. We present and discuss the compartmental organization of the Golgi stacks with regards to complex polysaccharide assembly and secretion using immuno-electron microscopy and specific antibodies recognizing various sugar epitopes. We also discuss the significance of the recently identified Golgi-localized glycosyltransferases responsible for the biosynthesis of xyloglucan (XyG) and pectin.
Human Leukocyte Antigens and HIV Type 1 Viral Load in Early and Chronic Infection: Predominance of Evolving Relationships

Background During untreated, chronic HIV-1 infection, plasma viral load (VL) is a relatively stable quantitative trait that has clinical and epidemiological implications. Immunogenetic research has established various human genetic factors, especially human leukocyte antigen (HLA) variants, as independent determinants of VL set-point. Methodology/Principal Findings To identify and clarify HLA alleles that are associated with either transient or durable immune control of HIV-1 infection, we evaluated the relationships of HLA class I and class II alleles with VL among 563 seroprevalent Zambians (SPs) who were seropositive at enrollment and 221 seroconverters (SCs) who became seropositive during quarterly follow-up visits. After statistical adjustments for non-genetic factors (sex and age), two unfavorable alleles (A*3601 and DRB1*0102) were independently associated with high VL in SPs (p<0.01) but not in SCs. In contrast, favorable HLA variants, mainly A*74, B*13, B*57 (or Cw*18), and one HLA-A and HLA-C combination (A*30+Cw*03), dominated in SCs; their independent associations with low VL were reflected in regression beta estimates that ranged from −0.47±0.23 to −0.92±0.32 log10 in SCs (p<0.05). Except for Cw*18, all favorable variants had diminishing or vanishing association with VL in SPs (p≤0.86). Conclusions/Significance Overall, each of the three HLA class I genes had at least one allele that might contribute to effective immune control, especially during the early course of HIV-1 infection. These observations can provide a useful framework for ongoing analyses of viral mutations induced by protective immune responses.
Specific Domains in Yeast Translation Initiation Factor eIF4G Strongly Bias RNA Unwinding Activity of the eIF4F Complex toward Duplexes with 5′-Overhangs*

Background: In yeast, eIF4A and eIF4F are essential for efficient translation initiation, but our understanding of their mechanisms of action is rudimentary. Results: A detailed biochemical analysis of yeast eIF4A, alone and within eIF4F, is described. Conclusion: The eIF4G subunit confers specificity for unwinding duplexes with 5′-overhangs on yeast eIF4F. Significance: The observed 5′-end specificity may play a role in ribosomal scanning along mRNA. During eukaryotic translation initiation, the 43 S ribosomal pre-initiation complex is recruited to the 5′-end of an mRNA through its interaction with the 7-methylguanosine cap, and it subsequently scans along the mRNA to locate the start codon. Both mRNA recruitment and scanning require the removal of secondary structure within the mRNA. Eukaryotic translation initiation factor 4A is an essential component of the translational machinery thought to participate in the clearing of secondary structural elements in the 5′-untranslated regions of mRNAs. eIF4A is part of the 5′-7-methylguanosine cap-binding complex, eIF4F, along with eIF4E, the cap-binding protein, and the scaffolding protein eIF4G. Here, we show that Saccharomyces cerevisiae eIF4F has a strong preference for unwinding an RNA duplex with a single-stranded 5′-overhang versus the same duplex with a 3′-overhang or without an overhang. In contrast, eIF4A on its own has little RNA substrate specificity. Using a series of deletion constructs of eIF4G, we demonstrate that its three previously elucidated RNA binding domains work together to provide eIF4F with its 5′-end specificity, both by promoting unwinding of substrates with 5′-overhangs and inhibiting unwinding of substrates with 3′-overhangs. Our data suggest that the RNA binding domains of eIF4G provide the S. cerevisiae eIF4F complex with a second mechanism, in addition to the eIF4E-cap interaction, for directing the binding of pre-initiation complexes to the 5′-ends of mRNAs and for biasing scanning in the 5′ to 3′ direction.
Diurnal cycling of glutathione in marine phytoplankton: Field and culture studies

Glutathione is an abundant intracellular thiol that is involved in the detoxification of reactive oxygen species generated in the presence of light. We used short‐term continuous cultures of Emiliania huxleyi and Thalassiosira pseudonana to show that a diurnal light cycle causes intracellular glutathione to undergo at least twofold variations, with maximum concentrations occurring during light periods. Cysteine concentrations also appear to vary in E. huxleyi to a similar extent, with the highest concentrations occurring at night. A complementary field study conducted at Salt Pond in Falmouth, Massachusetts, yielded a similar diurnal cycle of glutathione concentrations in particulate samples. This cycling is important to consider when measuring particulate thiols in both culture and field studies and provides additional evidence that glutathione plays an important role as an antioxidant in eukaryotic marine phytoplankton.
Temporal and Spectral Variabilities of High-Energy Emission from Blazars Using Synchrotron Self-Compton Models

Multiwavelength observations of blazars such as Mrk 421 and Mrk 501 show that they exhibit strong short time variabilities in flarelike phenomena. Working from the homogeneous synchrotron self-Compton (SSC) model and assuming that time variability of the emission is initiated by changes in the injection of nonthermal electrons, we perform detailed temporal and spectral studies of a purely cooling plasma system using parameters appropriate to blazars. One important parameter is the total injected energy ℰ, and we show how the synchrotron and Compton components respond as ℰ varies. When the synchrotron and SSC components have comparable peak fluxes, we find that the SSC process contributes strongly to the electron cooling and that the whole system is nonlinear; thus, simultaneously solving electron and photon kinetic equations is necessary. In the limit of the injection-dominated situation when the cooling timescale is long, we find a unique set of model parameters that are fully constrained by observable quantities. In the limit of the cooling-dominated situation, TeV emissions arise mostly from a cooled electron distribution and the Compton scattering process is always in the Klein-Nishina regime, which gives the TeV spectrum a large curvature. Furthermore, even in a single-injection event, the multiwavelength light curves do not necessarily track each other because the electrons that are responsible for those emissions might have quite different lifetimes. We discuss in detail how one could infer important physical parameters using the observed spectra. In particular, we could infer the size of the emission region by looking for exponential decay in the light curves. We could also test the basic assumption of the SSC model by measuring the difference in the rate of peak energy changes of synchrotron and SSC peaks. We also show that the trajectory in the photon index-flux plane evolves clockwise or counterclockwise depending on the value of ℰ and the observed energy bands.
Application of piezoelectric macro-fiber-composite actuators for the suppression of noise transmission through curved glass plates

An investigation on the application of the piezoelectric Macro-Fiber-Composite (MFC) actuators for the suppression of the noise transmission through the curved glass plates is presented. It is known that when the incident sound wave in the air hits the glass plate or curved plate or shell, part of the acoustic wave is reflected, which makes the plate vibrate, and part of the wave is transmitted. It is easy to understand that the higher the flexural rigidity of the glass plate the bigger part of the acoustic sound wave is reflected than transmitted. This simple physical phenomenon can be profitably used for the suppression of the noise transmission through glass plates. The noise suppression effect is achieved using the MFC actuator, which is attached to the vibrating glass plate. When the piezoelectric MFC actuator is shunted by the active electronic circuit, which has a negative capacitance, it is possible to greatly suppress the vibration of the glass plate and also the noise transmission through the glass plate. The sound shielding efficiency of the glass plate is measured by the acoustic transmission loss (TL), which is expresed in decibel scale. If the amplitude of the window vibrations decreases, the value of TL increases. The effect of the glass plate geometry, and the electrical properties of the active shunt circuit on the enhancement of TL is analyzed using Finite Element Method numerical simulations. The comparison of the results of numerical simulations with acoustic measurements is presented. The possibility of the use of this method for the suppression of the noise transmission through the glass window plates is discussed.
Skeletal development is regulated by fibroblast growth factor receptor 1 signalling dynamics

Ligand-dependent signalling pathways have been characterised as having morphogen properties where there is a quantitative relationship between receptor activation and response, or threshold characteristics in which there is a binary switch in response at a fixed level of receptor activation. Here we report the use of a bacterial artificial chromosome (BAC)-based transgenic system in which a hypermorphic mutation has been introduced into the murine Fgfr1 gene. These mice exhibit cranial suture and sternal fusions that are exacerbated when the BAC copy number is increased. Surprisingly, increasing mutant BAC copy number also leads to the de novo appearance of digit I polydactyly in the hind limb and transformations of the vertebrae. Polydactyly is accompanied by a reduction of programmed cell death in the developing hind limb. Candidate gene analysis reveals downregulation of Dkk1 in the digit I field and upregulation of Wnt5a and Hoxd13. These findings show that Fgfr1-mediated developmental pathways exhibit differing signalling dynamics, whereby development of the cranial sutures and sternum follows a morphogen mode, whereas development of the vertebral column and the hind limbs has threshold signalling properties.
Induction of IL-10 and TGFβ from CD4+CD25+FoxP3+ T Cells Correlates with Parasite Load in Indian Kala-azar Patients Infected with Leishmania donovani

Background Visceral leishmaniasis (VL) is distinguished by a complex interplay of immune response and parasite multiplication inside host cells. However, the direct association between different immunological correlates and parasite numbers remains largely unknown. Methodology/Principal Findings We examined the plasma levels of different disease promoting/protective as well as Th17 cytokines and found IL-10, TGFβ and IL-17 to be significantly correlated with parasite load in VL patients (r = 0.52, 0.53 and 0.51 for IL-10, TGFβ and IL-17, respectively). We then extended our investigation to a more antigen-specific response and found leishmanial antigen stimulated levels of both IL-10 and TGFβ to be significantly associated with parasite load (r = 0.71 and 0.72 for IL-10 and TGFβ respectively). In addition to cytokines we also looked for different cellular subtypes that could contribute to cytokine secretion and parasite persistence. Our observations manifested an association between different Treg cell markers and disease progression as absolute numbers of CD4+CD25+ (r = 0.55), CD4+CD25hi (r = 0.61) as well as percentages of CD4+CD25+FoxP3+ T cells (r = 0.68) all correlated with parasite load. Encouraged by these results, we investigated a link between these immunological components and interestingly found both CD4+CD25+ and CD4+CD25+FoxP3+ Treg cells to secrete significantly (p<0.05) higher amounts of not only IL-10 but also TGFβ in comparison to corresponding CD25- T cells. Conclusions/Significance Our findings shed some light on source(s) of TGFβ and suggest an association between these disease promoting cytokines and Treg cells with parasite load during active disease. Moreover, the direct evidence of CD4+CD25+FoxP3+ Treg cells as a source of IL-10 and TGFβ during active VL could open new avenues for immunotherapy towards cure of this potentially fatal disease.
More Heat Than Light: A Critical Assessment of the Same-Sex Parenting Literature, 1995–2013

Same-sex marriage is one of the great policy issues of our time, and part of this debate hinges on the ability of same-sex couples to parent. Most gay parenting studies conclude that children raised by gay parents perform as well, if not better, than their counterparts in heterosexual families. This conclusion, which may or may not be true, is not scientifically warranted because of various limitations: Some results are misreported; most of the literature is exploratory and made up of small qualitative samples, biased data, and other research design failures; the studies concentrate on lesbian families; and outcome measures have been limited. Although these problems prevent scientific generalizations, social scientists have treated the preliminary, nonconclusive research as authoritative. Quite naturally, those within public policy circles have adopted this unwarranted position. Regardless of what science ultimately demonstrates about same-sex family structure, it is important to safeguard the research process from political pressures: either anti-gay marriage or pro-gay rights.
Physical Activity Intensity, Lesson Context, and Teacher Interactions During an Unstructured Afterschool Physical Activity Program.

BACKGROUND Afterschool programs are promising arenas to improve youth physical activity (PA) levels. During the school year for 2012-2013, 5 elementary schools from a low-socioeconomic status (SES) school district in southern Colorado participated in evaluation of the afterschool program entitled Keep It Moving! (KIM). METHODS In this cross-sectional analysis we sought to evaluate the relationships among participant PA, teacher interaction, and lesson context during an unstructured afterschool PA program. Participants were third-fifth grade students enrolled in the KIM program at the 5 participating elementary schools and were assessed utilizing accelerometers and direct observation with the System for Observing Fitness Instruction Time (SOFIT). RESULTS Program participants wore the accelerometer 37.1 ± 5.4 min session(-1). Approximately half of the time was spent in light PA (LPA) and 15.7 ± 5.3 min session(-1) in moderate to vigorous PA (MVPA). Game play was positively associated with LPA and negatively associated with MVPA. When teachers did not promote PA with students there was a positive association with sedentary activity (SA) and a negative association with MVPA. CONCLUSIONS Lesson context and teacher interactions may be important factors associated with PA intensity of afterschool PA programming. Future research should address whether structured PA curricula may improve quality of afterschool PA programming.