Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel primers for complete mitochondrial cytochrome b gene sequencing in mammals

Sequence‐based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high‐scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high‐quality reference data can improve the reliability of sequence‐based species identification.
Use of T2‐weighted susceptibility contrast MRI for mapping the blood volume in the glioma‐bearing rat brain

The aim of this work was to evaluate the potential of T2‐weighted, steady‐state susceptibility‐enhanced contrast magnetic resonance imaging (MRI), to characterize brain tumor heterogeneity and tumor vascularization. In vivo T2‐weighted MRI experiments were carried out on normal rats (n = 11) and rats bearing C6 glioma (n = 17), before and after the injection of a remanent superparamagnetic contrast agent. The ΔR2 variations of the transverse relaxation rate due to the injection of the contrast agent were used to generate relative cerebral blood volume (CBV) maps. Contrast enhancement of the tumor was shown to reflect tissue vascularization rather than leakage of the blood‐brain barrier. The quantitative results clearly show the heterogeneity of tumor vascularization and reveal a high vessel density in the peripheral area (CBVper ∝ 17.2 ± 2.3 sec−1) and a low vessel density in the central area of the tumor (CBVcen ∝ 2.5 ± 0.5 sec−1). Magn Reson Med 42:754–761, 1999. © 1999 Wiley‐Liss, Inc.
Antimicrobial susceptibility pattern of Corynebacterium striatum

The in vitro activities of 16 antimicrobial agents against 86 strains of Corynebacterium striatum were evaluated by microdilution using cation-adjusted Mueller-Hinton broth. MICs at which 90% of strains were inhibited were 0.06 microgram/ml for teicoplanin, 1 microgram/ml for vancomycin, 0.03 to 8 micrograms/ml for beta-lactams, 8 micrograms/ml for sparfloxacin, 16 micrograms/ml for ciprofloxacin, 16/304 micrograms/ml for co-trimoxazole (trimethoprim-sulfamethoxazole), 64 micrograms/ml for tetracycline, 128 micrograms/ml for gentamicin, and > 128 micrograms/ml for amikacin, erythromycin, and rifampin.
Wide-Ranging Effects of the Yeast Ptc1 Protein Phosphatase Acting Through the MAPK Kinase Mkk1

The Saccharomyces cerevisiae type 2C protein phosphatase Ptc1 is required for a wide variety of cellular functions, although only a few cellular targets have been identified. A genetic screen in search of mutations in protein kinase–encoding genes able to suppress multiple phenotypic traits caused by the ptc1 deletion yielded a single gene, MKK1, coding for a MAPK kinase (MAPKK) known to activate the cell-wall integrity (CWI) Slt2 MAPK. In contrast, mutation of the MKK1 paralog, MKK2, had a less significant effect. Deletion of MKK1 abolished the increased phosphorylation of Slt2 induced by the absence of Ptc1 both under basal and CWI pathway stimulatory conditions. We demonstrate that Ptc1 acts at the level of the MAPKKs of the CWI pathway, but only the Mkk1 kinase activity is essential for ptc1 mutants to display high Slt2 activation. We also show that Ptc1 is able to dephosphorylate Mkk1 in vitro. Our results reveal the preeminent role of Mkk1 in signaling through the CWI pathway and strongly suggest that hyperactivation of Slt2 caused by upregulation of Mkk1 is at the basis of most of the phenotypic defects associated with lack of Ptc1 function.
Comparison of HIV‐1 drug‐resistance genotyping by ultra‐deep sequencing and sanger sequencing using clinical samples

Sanger population sequencing (SPS) is the reference technique to monitor HIV‐1‐infected patients’ therapy. Ultra‐deep sequencing (UDS), which allows quantitative detection of drug resistance mutations, may be an alternative method. The study aimed to compare reproducibility and predictions of UDS versus SPS in a routine setting. A control containing low‐abundance variants was repeatedly tested and clinical plasma samples from 100 patients were prospectively assayed by SPS and UDS using the Roche 454 system. Complete analysis by UDS was available for 88% of samples with various viral loads and subtypes. Comparison of detection thresholds found that SPS sensitivity was variable. Variations found by UDS between 5% to >20% were detected by SPS in 25% to more than 80% of samples. At the 5% cut‐off, disagreements were rare and in most cases UDS detected an additional protease secondary mutation, suggesting a possible resistance to a protease inhibitor according to the 2015 ANRS algorithm. Mutations found on reverse transcriptase by only UDS were often explained by previous therapy. UDS with a variant detection threshold at 5% might allow therapy management with minimal differences compared to population sequencing while providing additional information for further determination of pertinent cutoff values for specific resistance mutations.
PHOTON EXTREMITY ABSORBED DOSE AND KERMA CONVERSION COEFFICIENTS FOR CALIBRATION GEOMETRIES

Absorbed dose and dose equivalent conversion coefficients are routinely used in personnel dosimetry programs. These conversion coefficients can be applied to particle fluences or to measured air kerma values to determine appropriate operational monitoring quantities such as the ambient dose equivalent or personal dose equivalent for a specific geometry. For personnel directly handling materials, the absorbed dose to the extremities is of concern. This work presents photon conversion coefficients for two extremity calibration geometries using finger and wrist/arm phantoms described in HPS N13.32. These conversion coefficients have been calculated as a function of photon energy in terms of the kerma and the absorbed dose using Monte Carlo techniques and the calibration geometries specified in HPS N13.32. Additionally, kerma and absorbed dose conversion coefficients for commonly used x-ray spectra and calibration source fields are presented. The kerma values calculated in this work for the x-ray spectra and calibration sources compare well to those listed in HPS N13.32. The absorbed dose values, however, differ significantly for higher energy photons because charged particle equilibrium conditions have not been satisfied for the shallow depth. Thus, the air-kerma-to-dose and exposure-to-dose conversion coefficients for 137Cs and 60Co listed in HPS N13.32 overestimate the absorbed dose to the extremities. Applying the conversion coefficients listed in HPS N13.32 for 137Cs, for example, would result in an overestimate of absorbed dose of 62% for the finger phantom and 55% for the wrist phantom.
Clinical predictors and outcomes for patients requiring tracheostomy in the intensive care unit.

OBJECTIVE To identify clinical predictors for tracheostomy among patients requiring mechanical ventilation in the intensive care unit (ICU) setting and to describe the outcomes of patients receiving a tracheostomy. DESIGN Prospective cohort study. SETTING Intensive care units of Barnes-Jewish Hospital, an urban teaching hospital. PATIENTS 521 patients requiring mechanical ventilation in an ICU for >12 hours. INTERVENTIONS Prospective patient surveillance and data collection. MEASUREMENTS AND MAIN RESULTS The main variables studied were hospital mortality, duration of mechanical ventilation, length of stay in the ICU and the hospital, and acquired organ-system derangements. Fifty-one (9.8%) patients received a tracheostomy. The hospital mortality of patients with a tracheostomy was statistically less than the hospital mortality of patients not receiving a tracheostomy (13.7% vs. 26.4%; p = .048), despite having a similar severity of illness at the time of admission to the ICU (Acute Physiology and Chronic Health Evaluation [APACHE] II scores, 19.2 +/- 6.1 vs. 17.8 +/- 7.2; p = .173). Patients receiving a tracheostomy had significantly longer durations of mechanical ventilation (19.5 +/- 15.7 days vs. 4.1 +/- 5.3 days; p < .001) and hospitalization (30.9 +/- 18.1 days vs. 12.8 +/- 10.1 days; p < .001) compared with patients not receiving a tracheostomy. Similarly, the average duration of intensive care was significantly longer among the hospital nonsurvivors receiving a tracheostomy (n = 7) compared with the hospital nonsurvivors without a tracheostomy (n = 124; 30.9 +/- 16.3 days vs. 7.9 +/- 7.3 days; p < .001). Multiple logistic regression analysis demonstrated that the development of nosocomial pneumonia (adjusted odds ratio [AOR], 4.72; 95% confidence interval [CI], 3.24-6.87; p < .001), the administration of aerosol treatments (AOR, 3.00; 95% CI, 2.184.13; p < .001), having a witnessed aspiration event (AOR, 3.79; 95% CI, 2.30-6.24; p = .008), and requiring reintubation (AOR, 2.21; 95% CI, 1.54-3.18; p = .028) were variables independently associated with patients undergoing tracheostomy and receiving prolonged ventilatory support. Among the 44 survivors receiving a tracheostomy in the ICU, 38 (86.4%) were alive 30 days after hospital discharge and 31 (70.5%) were living at home. CONCLUSIONS Despite having longer lengths of stay in the ICU and hospital, patients with respiratory failure who received a tracheostomy had favorable outcomes compared with patients who did not receive a tracheostomy. These data suggest that physicians are capable of selecting critically ill patients who most likely will benefit from placement of a tracheostomy. Additionally, specific clinical variables were identified as risk factors for prolonged ventilatory assistance and the need for tracheostomy.
Diagnostic utility of 5‐hydroxymethylcytosine immunohistochemistry in melanocytic proliferations

Decreased hydroxymethylated cytosine (5‐hydroxymethycytosine, 5‐hmC) is reported to correlate with melanocyte dysplasia. The purpose of this study was to assess the diagnostic utility of this observation. 5‐hmC immunohistochemistry was performed on tissue microarrays containing 171‐melanocytic lesions from two different institutions. An immunohistochemical staining score representing the percentage and intensity of nuclear staining was assigned. The performance characteristics of 5‐hmC immunohistochemistry for discriminating between a nevus and melanoma were determined. Additional cases of melanoma arising in a nevus (n = 8), nodal nevi (n = 5) and melanoma micrometastases to a lymph node (n = 6) were also assessed. Pronounced 5‐hmC loss was observed in melanomas when compared with nevi (mean ± standard deviation = 6.71 ± 11.78 and 55.19 ± 23.66, respectively, p < 0.0001). While the mean immunohistochemical staining score values for melanocytic nevi and melanoma were distinct, there was considerable variability in immunohistochemical staining score within a single diagnostic category. The sensitivity and specificity of this assay for nevus vs. melanoma is 92.74 and 97.78%, respectively. Distinct biphasic staining patterns were observed in cases of melanoma arising in association with a nevus. Relative changes of 5‐hmC expression within a single lesion may be more informative than absolute values when using 5‐hmC as a diagnostic adjunct.
A novel protein, LcrQ, involved in the low-calcium response of Yersinia pseudotuberculosis shows extensive homology to YopH

The plasmid-encoded yop genes of pathogenic yersiniae are regulated by the environmental stimuli calcium and temperature. A novel protein, LcrQ, which exhibits a key function in the negative calcium-controlled pathway, was identified. DNA sequence analysis revealed that LcrQ has a molecular mass of 12,412 daltons and its isoelectric point is 6.51. Overexpression of LcrQ in trans in wild-type Yersinia pseudotuberculosis YPIII(pIB102) changed the phenotype from calcium dependence to calcium independence and inhibited Yop expression. LcrQ is expressed from a monocistronic operon. Trans overexpression of LcrQ in yopN and lcrH mutants affected the phenotype of the yopN mutant (temperature sensitive to calcium independence) but not that of the lcrH mutant (temperature sensitive), suggesting that LcrQ acts between YopN and LcrH in the calcium-regulated pathway. An lcrQ mutant was found to be temperature sensitive for growth and showed derepressed Yop expression at 37 degrees C in the presence of calcium in the growth medium. During these culture conditions, the lcrQ mutant secreted only LcrV and YopD into the culture supernatant. Removal of Ca2+ from the growth medium resulted in a Yop expression pattern of the mutant that was identical to that of the wild-type strain. The LcrQ protein was recovered from the culture supernatant. LcrQ shows 42% identity to the first 128 amino acids of the YopH virulence protein.
Phase II evaluation of fluorouracil and recombinant α‐2a‐interferon in previously untreated patients with pancreatic adenocarcinoma

Background. Based on initial encouraging results of the combination of 5‐fluorouracil (5‐FU) with recombinant α‐2a‐interferon (rα‐2a‐IFN) in the treatment of advanced colorectal carcinomas, a clinical trial was conducted using 5‐FU with rα‐2a‐IFN in 49 patients with advanced pancreatic adenocarcinoma.
Clinical, Functional, and Radiographic Differences Among Juvenile-onset, Adult-onset, and Late-onset Ankylosing Spondylitis

Objective. The aim of our study was to compare the clinical, functional, and radiographic outcomes at different ages of onset in patients with ankylosing spondylitis (AS). Methods. A total of 546 patients were enrolled consecutively and classified into 3 groups based on their age at symptom onset: (1) juvenile-onset AS (age ≤ 16 years; JoAS); (2) adult-onset AS (> 16 but < 40 years; AoAS); and (3) late-onset AS (≥ 40 years; LoAS). We compared the differences among the 3 groups. OR for disease outcomes were calculated and adjusted for sex, HLA-B27, and disease duration. Results. There were 67 patients (12.3%) with JoAS, 460 (84.2%) with AoAS, and 19 (3.5%) with LoAS. Male sex and HLA-B27 were associated with a younger age at onset (p < 0.001). Compared to patients with AoAS, patients with JoAS were more likely to present with peripheral arthritis, while patients with JoAS and LoAS were less likely to have back pain at the onset of AS (p < 0.05). After controlling for multiple covariates, JoAS was found to be associated with a worse functional outcome and global assessment, and a high serum immunoglobulin A level (p < 0.05). Patients with JoAS had less lumbar spinal radiographic severity (p < 0.05). There were no statistical differences in clinical or functional outcome between the LoAS and AoAS groups. None of the LoAS patients had radiographic hip involvement. Conclusion. Sex and HLA-B27 are significantly associated with age at onset of AS. Both JoAS and LoAS have their distinctive symptoms/signs at onset and different disease outcomes.
Temozolomide in Patients with Glioblastoma at Second Relapse after First Line Nitrosourea-Procarbazine Failure: A Phase II Study

Objectives: To investigate the efficacy of temozolomide (TMZ) in relationship to progression free survival at 6 months (PFS-6), median time to progression (TTP), response rate and toxicity, a phase II study was conducted in patients with recurrent glioblastoma multiforme (GBM) following surgery plus radiotherapy and a first-line regimen based on nitrosourea, procarbazine and vincristine. Methods: Forty-two patients with GBM were administered TMZ at the dose of 150 mg/m2/daily for 5 days every 4 weeks. Results: The PFS-6 and at 12 months (PFS-12) was 24% (95% Confidence Interval [CI] = 14–42%) and 8% (CI = 2–27%), respectively, with a median TTP of 11.7 weeks (CI = 9–22 weeks). The response was assessed in all 42 patients; we observed 2 complete responses (CR) (4.7%), 6 partial responses (PR) (14.3%), and 9 stable disease (SD) (21.4%), with CR+PR = 19% (CI = 7–31%). Conclusion: TMZ as a second line regimen is a valid option in patients with heavily pretreated GBM.
Does Hyperbaric Oxygen Therapy Work in Facilitating Acute Wound Healing: A Systematic Review

Background: Adjunctive hyperbaric oxygen therapy is a safe and effective modality with which to increase tissue oxygenation and aid in healing of difficult wounds. The majority of the literature surrounding hyperbaric oxygen therapy supports its use in chronic wounds, but its use in acute wounds, flaps, and grafts is less well supported. Methods: The authors reviewed the Ovid, PubMed, and Cochrane Library databases, and selected studies, level III and above, using hyperbaric oxygen therapy in the treatment of complicated acute wounds, flaps, and grafts. Results: A total of eight studies were found to meet criteria for evaluation of adjunctive hyperbaric oxygen therapy in the treatment of complicated acute wounds, flaps, and grafts. Conclusions: When combined with standard wound management principles, hyperbaric oxygen therapy can augment healing in complicated acute wounds. However, it is not indicated in normal wound management. Further investigation is required before it can be recommended as a mainstay in adjuvant wound therapy. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, II.
Circulating L-selectin levels and endothelial CD34 expression in inflammatory bowel disease

Objective:Soluble L-selectin (sL-selectin) concentrations are positively correlated with disease activity in ulcerative colitis (UC) but not in Crohn's disease (CD). This difference in sL-selectin regulation could be due to a disease specific regulation of L-selectin ligands. The aim of this study was to compare levels of circulating sL-selectin, expression of the L-selectin ligand CD34 in the affected colon, and inflammatory bowel disease activity.Methods:Twenty-three patients with UC, 16 patients with CD, and 18 control subjects were included in the study. In blood samples concentrations of serum sL-selectin were determined by an ELISA technique. In colonoscopically obtained biopsies, CD34 expression was evaluated by immunohistochemical methods using monoclonal CD34 antibodies. Disease activity was determined by a clinical semiquantitative scale.Results:sL-selectin levels were found to be significantly increased along with increasing disease activity in UC (p < 0.001) but not in CD (p > 0.05) patients. UC patients with quiescent and severe disease activity had significantly lower (p < 0.005) and higher (p < 0.002) sL-selectin concentrations than controls, respectively. CD34 expression was found to be increased in both disease groups as compared with controls (p < 0.05). Conclusion:A disease-specific regulation of CD34 was not found as an explanation for the distinction in sL-selectin regulation. In the light of recent reports on low sL-selectin in other diseases, it is suggested instead that ongoing neutrophil activation may be the reason for low sL-selectin concentrations during quiescent disease stages, whereas chemokine secretion could explain the increased levels of sL-selectin associated with severe disease activity.
Involvement of the Urokinase Kringle Domain in Lipopolysaccharide-Induced Acute Lung Injury1

Urokinase plasminogen activator (uPA) plays a major role in fibrinolytic processes and also can potentiate LPS-induced neutrophil activation through interactions with its kringle domain (KD). To investigate the role of the uPA KD in modulating acute inflammatory processes in vivo, we cloned and then developed Abs to the murine uPA KD. Increased pulmonary expression of uPA and the uPA KD was present in the lungs after LPS exposure. Administration of anti-kringle Abs diminished LPS-induced up-regulation of uPA and uPA KD in the lungs, and also decreased the severity of LPS-induced acute lung injury, as determined by development of lung edema, pulmonary neutrophil accumulation, histology, and lung IL-6, MIP-2, and TNF-α cytokine levels. These proinflammatory effects of the uPA KD appeared to be mediated through activation of Akt and NF-κB. The present studies indicate that the uPA KD plays a major role in the development of TLR4-mediated acute inflammatory processes, including lung injury. Blockade of the uPA KD may prevent the development or ameliorate the severity of acute lung injury induced through TLR4-dependent mechanisms, such as would occur in the setting of Gram-negative pulmonary or systemic infection.
Brief Report: Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure

Danon disease is a familial cardiomyopathy associated with impaired autophagy due to mutations in the gene encoding lysosomal‐associated membrane protein type 2 (LAMP‐2). Emerging evidence has highlighted the importance of autophagy in regulating cardiomyocyte bioenergetics, function, and survival. However, the mechanisms responsible for cellular dysfunction and death in cardiomyocytes with impaired autophagic flux remain unclear. To investigate the molecular mechanisms responsible for Danon disease, we created induced pluripotent stem cells (iPSCs) from two patients with different LAMP‐2 mutations. Danon iPSC‐derived cardiomyocytes (iPSC‐CMs) exhibited impaired autophagic flux and key features of heart failure such as increased cell size, increased expression of natriuretic peptides, and abnormal calcium handling compared to control iPSC‐CMs. Additionally, Danon iPSC‐CMs demonstrated excessive amounts of mitochondrial oxidative stress and apoptosis. Using the sulfhydryl antioxidant N‐acetylcysteine to scavenge free radicals resulted in a significant reduction in apoptotic cell death in Danon iPSC‐CMs. In summary, we have modeled Danon disease using human iPSC‐CMs from patients with mutations in LAMP‐2, allowing us to gain mechanistic insight into the pathogenesis of this disease. We demonstrate that LAMP‐2 deficiency leads to an impairment in autophagic flux, which results in excessive oxidative stress, and subsequent cardiomyocyte apoptosis. Scavenging excessive free radicals with antioxidants may be beneficial for patients with Danon disease. In vivo studies will be necessary to validate this new treatment strategy. Stem Cells 2015;33:2343–2350