Miracle-dz/UniFAR-FTUs huggingface dataset:
A synthetic hybrid promoter for D-xylonate production at low pH in the tolerant yeast Candida glycerinogenes

ABSTRACT The tolerant yeast Candida glycerinogenes, with high D-xylonate and low-pH tolerances, was used as the host for D-xylonate production at low pH in this study. A low-pH inducible promoter, pGUKd, was engineered using the core promoter of the glyceraldehyde-3-phosphate dehydrogenase gene (pGAP) combined with the upstream activating sequence of the promoter of the guanylate kinase gene (pGUK1) that had substituted pH-responsive TF binding sites. The recombinant cells that expressed GFP from the hybrid promoter pGUKd displayed dramatically increased fluorescence intensity at pH 2.5, thus verifying that pGUKd is a low-pH inducible promoter. The promoter pGUKd was then used to express the D-xylose dehydrogenase gene xylB, resulting in increased expression levels of xylB at low pH. The recombinant protein exhibited higher specific activities under lower pH conditions and produced 38 g/l D-xylonate at pH 2.5. This rate is much higher than that produced by fermentation at pH 5.5. These results suggest that the novel hybrid promoter pGUKd functions to direct the production of D-xylonate at low pH, and we provide a candidate genetic tool for the stress tolerant yeast C. glycerinogenes.
Spatial Distribution and Function of Sterol Regulatory Element-Binding Protein 1a and 2 Homo- and Heterodimers by In Vivo Two-Photon Imaging and Spectroscopy Fluorescence Resonance Energy Transfer

ABSTRACT Sterol regulatory element-binding proteins (SREBPs) are a subfamily of basic helix-loop-helix-leucine zipper proteins that regulate lipid metabolism. We show novel evidence of the in vivo occurrence and subnuclear spatial localization of both exogenously expressed SREBP-1a and -2 homodimers and heterodimers obtained by two-photon imaging and spectroscopy fluorescence resonance energy transfer. SREBP-1a homodimers localize diffusely in the nucleus, whereas SREBP-2 homodimers and the SREBP-1a/SREBP-2 heterodimer localize predominantly to nuclear speckles or foci, with some cells showing a diffuse pattern. We also used tethered SREBP dimers to demonstrate that both homo- and heterodimeric SREBPs activate transcription in vivo. Ultrastructural analysis revealed that the punctate foci containing SREBP-2 are electron-dense nuclear bodies, similar or identical to structures containing the promyelocyte (PML) protein. Immunofluorescence studies suggest that a dynamic interplay exists between PML, as well as another component of the PML-containing nuclear body, SUMO-1, and SREBP-2 within these nuclear structures. These findings provide new insight into the overall process of transcriptional activation mediated by the SREBP family.
Impact of immunosuppression on the incidence of early subclinical renal allograft rejection: implications for protocol biopsy policy

In order to determine the impact of immunosuppression (IS) on the incidence of early subclinical rejection (SCR), we studied two groups of patients receiving different immunosuppressive regimens. Patients received cyclosporin (CsA), azathioprine and prednisolone (group 1; n = 304) or IS according to immunological risk (group 2; n = 150). The highest‐risk patients received basiliximab induction, tacrolimus, mycophenolate mofetil (MMF) and prednisolone; medium‐risk patients CsA, MMF and prednisolone; low‐risk CsA, azathioprine and prednisolone. Protocol biopsies were performed in all patients, irrespective of graft function, on days 7 and 28 post‐transplantation. Only patients with good stable function at the time of biopsy were included for assessment of SCR. Group 2 patients showed significant reductions in total rejection frequency (32.6% vs. 57.2%, P = <0.0001) and SCR frequency in day 7 protocol biopsies (2% vs. 13%, P = <0.05). In group 2 patients, all SCRs, but not borderline changes, were treated. Untreated borderline changes did not have an adverse impact on graft function at 1 year post‐transplantation. New immunosuppressive regimens may reduce subclinical in addition to clinical rejection‐frequency, suggesting that the relative benefit of early protocol biopsies in detecting SCR is also reduced.
Sonographic appearance of epididymal microlithiasis

We report a case of epididymal microlithiasis that was diagnosed sonographically in a 75‐year‐old man undergoing scrotal sonographic examination to investigate right groin pain associated with an inguinal hernia. The sonographic appearance was that of multiple comet‐shaped foci of microcalcification throughout both epididymides, with associated comet‐tail artifacts. The testes had normal appearance with no evidence of testicular microlithiasis. The patient subsequently remained well after hernia repair. To our knowledge, epididymal microlithiasis has only previously been reported in a cadaveric study; the authors of that study hypothesized that the condition is caused by aging, with ischemia likely implicated in the pathogenesis. There are many other patterns of extratesticular calcification, including sperm granuloma, hematoma, and chronic epididymitis. We discuss how these differ in appearance from epididymal microlithiasis. Epididymal microlithiasis is a completely separate entity from testicular microlithiasis and should be recognized and dismissed by sonographers and radiologists. © 2007 Wiley Periodicals, Inc. J Clin Ultrasound, 2007
Restricted Expression of Shiga Toxin Binding Sites on Mucosal Epithelium of Mouse Distal Colon

ABSTRACT Shiga toxins (Stx) are some of the major virulence factors of enterohemorrhagic Escherichia coli strains such as serotype O157:H7. To explore how Stx might initially gain access to the bloodstream from sites of infection, frozen sections of mouse colon were immunohistochemically examined for binding sites for recombinant binding subunits (Stx1B). Binding sites were selectively expressed on the epithelium in the distal half of the mouse colon, whereas the proximal half did not exhibit any binding sites. In agreement with this observation, we also demonstrated the distal-part-restricted distribution of glycolipids that bind to Stx1B in the mouse colon. For comparison, the binding sites of several control lectins were also examined. Selective binding to the distal part of the colon was not seen with any other control lectins, including Griffonia simplicifolia lectin-I isolectin B4 (GS-I-B4), which shares α-galactose specificity with Stx1B. Partial overlapping of the specificities of Stx1B and GS-I-B4 was seen by assay with globotriose-conjugated multivalent ligands. The results indicate that Stx1B is stricter in the recognition of carbohydrate determinants than GS-I-B4 when examined with biological ligands.
Adhesion-dependent Signaling by Macrophage Migration Inhibitory Factor (MIF)*

Proper stimulation of cell cycle progression and DNA synthesis requires cooperating signals from integrin and growth factor receptors. We previously found that the proinflammatory peptide, macrophage migration inhibitory factor (MIF), functions as an autocrine mediator of growth factor-dependent ERK MAP kinase activation and cell cycle progression. We now report that MIF secretion is induced by cell adhesion to fibronectin in quiescent mouse fibroblasts. Adhesion-mediated release of MIF subsequently promotes integrin-dependent activation of MAP kinase, cyclin D1 expression, and DNA synthesis. Secretion of MIF requires protein kinase C activity, and recombinant MIF reconstitutes the activation of MAP kinases in the presence of protein kinase C inhibition. Finally, we show that cells deficient in MIF have significantly higher retinoblastoma tumor suppressor and lower E2F transcriptional activities. These results suggest that MIF is an important autocrine mediator of adhesion-dependent signaling events and may provide mechanistic insight into how MIF regulates proliferative and oncogenic processes.
Development and initial validation of the Vasculitis Damage Index for the standardized clinical assessment of damage in the systemic vasculitides.

OBJECTIVE To develop and validate the Vasculitis Damage Index (VDI) for the standardized clinical assessment of damage in the systemic vasculitides. METHODS Using a nominal group consensus approach, the Birmingham Vasculitis Group generated guiding principles for assessment of damage in all systemic vasculitides. Damage was defined as irreversible change resulting from scars. Consensus principles were developed into the VDI, including guidelines for use, a list of items of damage, and a glossary. RESULTS For 100 surviving patients with systemic vasculitis, the median VDI score at last observation was 3 (range 0-8). Within the Wegener's granulomatosis subgroup, the median VDI score for 12 non-survivors was higher than for 47 survivors (non-survivors median score 7, interquartile range 5-8 versus survivors median score 4, interquartile range 2-5; P = 0.003). VDI scores for 100 patients with systemic vasculitis increased from initial presentation to last observation by a median score of 3 (range 1-4; P < 0.001). The VDI assesses more items and is more sensitive to change than other indices of damage (P < 0.001). Using the VDI, trained observers can produce moderately consistent damage scores. CONCLUSION The VDI is a sensitive, reproducible, comprehensive, and credible clinical tool for quantifying damage. The data presented herein should enable further validation and testing of the VDI in specific vasculitic syndromes, and should facilitate the comparison of different therapies.
Contusion, dislocation, and distraction: primary hemorrhage and membrane permeability in distinct mechanisms of spinal cord injury.

OBJECT In experimental models of spinal cord injury (SCI) researchers have typically focused on contusion and transection injuries. Clinically, however, other injury mechanisms such as fracture-dislocation and distraction also frequently occur. The objective of the present study was to compare the primary damage in three clinically relevant animal models of SCI. METHODS Contusion, fracture-dislocation, and flexion-distraction animal models of SCI were developed. To visualize traumatic increases in cellular membrane permeability, fluorescein-dextran was infused into the cerebrospinal fluid prior to injury. High-speed injuries (approaching 100 cm/second) were produced in the cervical spine of deeply anesthetized Sprague-Dawley rats (28 SCI and eight sham treated) with a novel multimechanism SCI test system. The animals were killed immediately thereafter so that the authors could characterize the primary injury in the gray and white matter. Sections stained with H & E showed that contusion and dislocation injuries resulted in similar central damage to the gray matter vasculature whereas no overt hemorrhage was detected following distraction. Contusion resulted in membrane disruption of neuronal somata and axons localized within 1 mm of the lesion epicenter. In contrast, membrane compromise in the dislocation and distraction models was observed to extend rostrally up to 5 mm, particularly in the ventral and lateral white matter tracts. CONCLUSIONS Given the pivotal nature of hemorrhagic necrosis and plasma membrane compromise in the initiation of downstream SCI pathomechanisms, the aforementioned differences suggest the presence of mechanism-specific injury regions, which may alter future clinical treatment paradigms.
Who seeks treatment for alcohol dependence? Findings from the Australian National Survey of Mental Health and Wellbeing.

BACKGROUND This paper presents findings from the Australian National Survey of Mental Health and Wellbeing (NSMHWB) regarding prevalence and treatment seeking for Australians with DSM-IV alcohol dependence and examines the influence of alcohol use variables on treatment seeking. METHOD A standardised interview (including CIDI 2.1) was administered to a stratified random sample of 10,641 Australians aged 18 years and over. Demographic variables, common DSM-IV mental disorders, physical health status, perceived disability and treatment-seeking behaviour were assessed. Multiple logistic regression was used to ascertain the independent effects of all variables considered. RESULTS The prevalence of DSM-IV alcohol dependence was 4.1 % in this population, with 75 % being male and nearly 60 % in the 18-34 year age group. Variables that correlated independently with alcohol dependence were sex (male), age (young), not being in a married or de facto relationship and having any affective, anxiety or other substance use disorder. Functional disability did not correlate with a dependence diagnosis. Correlates of treatment seeking for those with dependence were sex (female) and having a comorbid affective disorder. Having a diagnosis of dependence and/or abuse and having more dependence symptoms did not predict treatment seeking. However, meeting either of two criteria assessing psychological, physical or social problems due to alcohol use tended to increase service use. CONCLUSIONS People with alcohol dependence do not perceive themselves as disabled and do not seek treatment. However, having a comorbid affective disorder or other problems directly attributable to alcohol use increases the likelihood that such individuals will seek treatment. Efforts should be made at the primary care level to encourage those engaged in harmful drinking practices to recognise the risks of such drinking and reduce it or seek treatment. Similarly, it is recommended that integrated services are enhanced at both primary and specialist levels in order that those with multiple problems are appropriately treated. Further research is required to refine measurement of disability and diagnoses of alcohol use disorders and to examine the relationship between disability and alcohol use.
Effects of a telephone-based psychosocial intervention for patients awaiting lung transplantation.

STUDY OBJECTIVES To test the efficacy of a tailored telephone-based intervention consisting of supportive counseling and cognitive behavioral techniques for individuals awaiting lung transplantation on measures of quality of life and general well-being. METHOD Patients were randomly assigned to either a telephone-based special intervention (SI; n = 36) for 8 weeks (average session length, 16.3 min) or a usual care (UC) control condition (n = 35) in which subjects received usual medical care but no special treatment or phone calls. At baseline, and immediately following the 8-week intervention, patients completed a psychometric test battery. SETTING Duke University Medical Center, Pulmonary Transplantation Program. PATIENTS Seventy-one patients with end-stage pulmonary disease listed for lung transplantation. PRIMARY OUTCOME MEASURES Measures of health-related quality of life (both general and disease-specific), general psychological well-being, and social support. RESULTS Multivariate analysis of covariance, adjusting for pretreatment baseline scores, age, gender, and time waiting on the transplant list, revealed that patients in the SI condition compared to the UC reported greater general well-being (p < 0.05), better general quality of life (p < 0.01), better disease-specific quality of life (p < 0.05), and higher levels of social support (p < 0.0001). CONCLUSION A brief, relatively inexpensive, telephone-based psychosocial intervention is an effective method for reducing distress and increasing health-related quality of life in patients awaiting lung transplantation.
A Salmonella protein that is required for resistance to antimicrobial peptides and transport of potassium.

The ability of invading pathogens to proliferate within host tissues requires the capacity to resist the killing effects of a wide variety of host defense molecules. sap mutants of the facultative intracellular parasite Salmonella typhimurium exhibit hypersensitivity to antimicrobial peptides, cannot survive within macrophages in vitro and are attenuated for mouse virulence in vivo. We conducted a molecular genetic analysis of the sapG locus and showed that it encodes a product that is 99% identical to the NAD+ binding protein TrkA, a component of a low‐affinity K+ uptake system in Escherichia coli. SapG exhibits similarity with other E. coli proteins implicated in K+ transport including KefC, a glutathione‐regulated efflux protein, and Kch, a putative transporter similar to eukaryotic K+ channel proteins, sapG mutants were killed by the antimicrobial peptide protamine in the presence of both high and low K+, indicating that protamine hypersensitivity is not due to K+ starvation. Strains with mutations in sapG and either sapJ or the sapABCDF operon were as susceptible as sapG single mutants, suggesting that the proteins encoded by these loci participate in the same resistance pathway. SapG may modulate the activities of SapABCDF and SapJ to mediate the transport of peptides and potassium.
Clustering by directions algorithm to narrow search queries

This article describes a novel algorithm called clustering by directions. This algorithm is designed to create a list of words which serve as suggestions for users of search engines how to modify their current search query. The algorithm focuses on preparing various suggestions. It concerns modifying queries by adding more words to them. A list of suggested words is presented to the user in a form of a tag cloud. Experiments which were performed with the algorithm show its usefulness.
Reduced phase error through optimized control of a superconducting qubit

Minimizing phase and other errors in experimental quantum gates allows higher fidelity quantum processing. To quantify and correct for phase errors, in particular, we have developed an experimental metrology - amplified phase error (APE) pulses - that amplifies and helps identify phase errors in general multilevel qubit architectures. In order to correct for both phase and amplitude errors specific to virtual transitions and leakage outside of the qubit manifold, we implement 'half derivative', an experimental simplification of derivative reduction by adiabatic gate (DRAG) control theory. The phase errors are lowered by about a factor of five using this method to {approx}1.6 deg. per gate, and can be tuned to zero. Leakage outside the qubit manifold, to the qubit |2> state, is also reduced to {approx}10{sup -4} for 20% faster gates.
Racial difference in lean mass distribution among reproductive-aged women.

OBJECTIVE Lean mass is an important determinant of bone mineral density (BMD) accrual, yet data regarding its correlates based on multiethnic premenopausal women are lacking. We examined the influence of age, race/ethnicity, and lifestyle variables on total and regional lean mass distribution in this population. DESIGN A cross-sectional study was conducted on 708 healthy Black, White, and Hispanic women aged 16-33 years who were seen in an outpatient clinic. In addition, 218 of these women were followed for up to 36 months to observe changes in the relevant variables. We measured body weight, height, and lean mass distribution using a digital scale, wall-mounted stadiometer, and dual-energy absorptiometry (DXA), respectively. Multiple linear regression and mixed-model regression analyses were used to model the relationship of age, race/ethnicity and lifestyle variables to total and regional lean mass. RESULTS For a given body mass index (BMI), Black women had higher total body lean mass (LM(total)) and leg lean mass (LM(leg)) than White and Hispanic women. Hispanic women had significantly lower LM(total), trunk lean mass (LM(trunk)), and LM(leg) than Black and White women. The difference between Blacks and Whites with regard to LM(total) significantly magnified with increasing BMI. Weight-bearing exercise and age at menarche were positively associated with lean mass variables, while parity was negatively associated with LM(leg). LM(total) and LM(trunk) increased over 36 months. Calcium intake was positively associated with increase in LM(totaI) over time. CONCLUSIONS Our study shows that racial differences exist in the distribution of lean mass for a given BMI among reproductive-aged women.
Traffic peccancy processing system based on image recognition

In this paper, we developed a traffic peccancy processing system. This system employed computer vision technique to monitor the traffic status and recognized the vehicles violating the traffic light, the vehicles stopping in the place where parking is not allowed, the vehicles crossing over the center real line of the traffic lanes and reversing in the driveway.
Factors that influence the acceptance of telemetry by emergency medical technicians in ambulances: an application of the extended technology acceptance model.

OBJECTIVE The aim of the study was to verify the effects of patient factors perceived by emergency medical technicians (EMTs) as well as their social and organizational factors on prehospital telemetry use intention based on the technology use intention and elaboration likelihood models. MATERIALS AND METHODS This is a retrospective empirical study. Questionnaires were developed on the basis of clinical factors of 72,907 patients assessed by prehospital telemetry from January 1, 2009 to April 30, 2012 by reviewing their prehospital medical care records and in-hospital medical records. Questionnaires regarding the social and organizational factors of EMTs were created on the basis of a literature review. To verify which factors affect the utilization of telemetry, we developed a partial least-squares route model on the basis of each characteristic. In total, 136 EMTs who had experience in using prehospital telemetry were surveyed from April 1 to April 7, 2013. Reliability, validity, hypotheses, and the model goodness of fit of the study tools were tested. RESULTS The clinical factors of the patients (path coefficient=-0.12; t=2.38), subjective norm (path coefficient=0.18; t=2.63), and job fit (path coefficient=0.45; t=5.29) positively affected the perceived usefulness (p<0.010). Meanwhile, the clinical factors of the patients (path coefficients=-0.19; t=4.46), subjective norm (path coefficient=0.08; t=1.97), loyalty incentives (path coefficient=-0.17; t=3.83), job fit (path coefficient=-0.32; t=7.06), organizational facilitations (path coefficient=0.08; t=1.99), and technical factors (i.e., usefulness and ease of use) positively affected attitudes (path coefficient=0.10, 0.58; t=2.62, 5.81; p<0.010). Attitudes and perceived usefulness significantly positively affected use intention. CONCLUSIONS Factors that influence the use of telemetry by EMTs in ambulances included patients' clinical factors, as well as complex organizational and environmental factors surrounding the EMTs' occupational environments. This suggests that the rapid use intention and dissemination of such systems require EMTs to be supported at both the technical and organizational levels.