Miracle-dz/UniFAR-FTUs huggingface dataset:
Subcellular Distribution and Characterization of Rat Pancreatic Phospholipase D Isoforms

This study was undertaken to characterize the biochemical properties of rat pancreatic phospholipase D (PLD). Based on Western blot analysis of pancreas subcellular fractions, PLD1 was detected as a protein of 120 kDa associated with the microsomal fraction, whereas PLD2 appeared as a 105-kDa protein enriched in the microvesicular fraction. In these fractions, a low level of PLD activity was measured with an exogenous substrate containing phosphatidylinositol-4,5-bisphosphate (PIP2), unresponsive to guanosine triphosphate (GTP)&ggr;S and adenosine diphosphate (ADP)-ribosylation factor (ARF). Addition of unsaturated but not saturated fatty acids stimulated an oleate-dependent PLD activity that colocalized with the PLD1 enzyme in the crude plasma membrane and microsomal fractions. The transphosphatidylation reaction was maximal with either 200–400 m M (1.2–2.3%) ethanol or 25 m M (0.23%) 1-butanol, with an optimal pH between 6.5 and 7.2. Lipids extracted from the pancreatic membranes were potent inhibitors of the HL60 cell PLD activity when compared with those isolated from HL60 cells. Oleate-dependent PLD activity was less susceptible to these inhibitions. A phospholipase A1 (PLA1) activity hydrolyzing phosphatidylethanol also was found in the pancreatic membrane fractions and was nearly absent in the HL60 cells. This activity was completely inhibited by 400 n M tetrahydrolipstatin (THL), a lipase inhibitor. Pancreatic PLD1 and PLD2 activities could be measured after a chromatographic separation from microsomal membranes and high-speed supernatants, respectively. Activities of both enzymes were inhibited by oleate and required the presence of PIP2 in the substrate vesicles. ARF1 strongly activated PLD1 in a dose-dependent manner, and PLD2 was slightly responsive. Indirect immunofluorescence revealed that PLD2 is distributed throughout the pancreas, with a more intense staining in the islets. This study presents for the first time biochemical characteristics of the pancreatic PLD activities and shows the presence of oleate-dependent PLD1 and PLD2 activities, as well as PLD1 and PLD2 proteins in this gland.
Replication of vesicular stomatitis virus in murine spleen cells: enrichment of the virus-replicating lymphocytes and analysis of replication restriction

Vesicular stomatitis virus (Indiana strain) will only grow in T lymphocytes which have been stimulated to undergo cell division. Evidence is presented that a considerable enrichment of the vesicular stomatitis virus-replicating T cells may be accomplished in the mouse spleen by passing the spleen cells over glass wool columns. By using this procedure experiments were performed to study the nature of the block in vesicular stomatitis virus replication in unstimulated (nonpermissive) versus mitogen-stimulated (permissive) splenic T cells. The results show that, as is the case in permissive T-cell lines, stimulated normal T cells allow the synthesis of the 42S virion ribonucleic acid.
Using long‐term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin‐treated mouse gut

Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole‐genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long‐term adaptation of an E. coli natural isolate, the streptomycin‐resistant strain 536, in the digestive tract of streptomycin‐treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D‐galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that ‘evolve and sequence’ approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.
Conditional Probability of Long-term Survival After Liver Resection for Intrahepatic Cholangiocarcinoma: A Multi-institutional Analysis of 535 Patients.

IMPORTANCE Whereas conventional actuarial overall survival (OS) estimates rely exclusively on static factors determined around the time of surgery, conditional survival (CS) estimates take into account the years that a patient has already survived. OBJECTIVE To define the CS of patients following liver resection for intrahepatic cholangiocarcinoma (ICC). DESIGN, SETTING, AND PARTICIPANTS Between January 1, 1990, and December 31, 2013, a total of 535 patients who underwent resection of ICC were identified from an international multi-institutional database. In this retrospective international study conducted from January to June 2014, clinicopathological characteristics, operative details, and long-term survival data were analyzed. Conditional survival estimates were calculated as the probability of survival for an additional 3 years. INTERVENTION Resection of ICC. MAIN OUTCOMES AND MEASURES Overall survival and CS. RESULTS While actuarial OS decreased over time from 39% at 3 years to 16% at 8 years (P = .002), the 3-year CS (CS₃) increased over time among those patients who survived. The CS₃ at 5 years-the probability of surviving to postoperative year 8 after having already survived to postoperative year 5-was 65% compared with 8-year OS of 16% (P = .002). Factors that were associated with worse OS included larger tumor size (hazard ratio [HR], 1.02; 95% CI, 1.00-1.05; P = .05), multifocal disease (HR, 1.49; 95% CI, 1.19-1.86; P = .01), lymph node metastasis (HR, 2.21; 95% CI, 1.67-2.93; P < .01), and vascular invasion (HR, 1.39; 95% CI, 1.10-1.75; P = .006). The calculated CS₃ exceeded the actuarial survival for all high-risk subgroups. For example, patients with lymph node metastasis had an actuarial OS of 11% at 6 years vs a CS₃ of 49% at 3 years (Δ38%). Similarly, patients with vascular invasion had an actuarial OS of 15% at 6 years compared with a CS₃ of 50% at 3 years (Δ35%). CONCLUSIONS AND RELEVANCE Conditional survival estimates may provide critical quantitative information about the changing probability of survival over time among patients undergoing liver resection for ICC. Therefore, such estimates can be of significant value to patients and health care professionals.
Maternal, infant, and delivery factors associated with neonatal thyroid hormone status.

BACKGROUND Thyroid function is dynamic during the perinatal period with many factors potentially influencing maternal, fetal and neonatal TSH and thyroid hormone levels. We sought to identify the impact of numerous maternal, fetal and delivery attributes on thyroid parameters in newborns. METHODS This was a cross sectional study of 300 newborns. Detailed information was obtained from medical records and multiple characteristics from the record were tested as predictors of cord blood serum total T4, free T4 and TSH and infant T4 levels from the Maryland newborn screening program. MAIN OUTCOME Outcomes are levels of thyroid stimulating hormone (TSH), thyroxine (T(4)), and free T(4) in newborn cord serum and total T(4) in postnatal heelstick bloodspot samples. RESULTS Multivariate models identified a number of variables that are independently associated with thyroid hormone levels: higher birth order (lower cord TSH); older maternal age (lower cord total T(4)); pregnancy-induced hypertension and/or preeclampsia (lower cord total T(4) and free T(4)); gestational diabetes (higher cord free T(4)); sexually transmitted disease during pregnancy (lower cord TSH); alcohol use during pregnancy (lower cord TSH); thyroid condition/medications (higher bloodspot total T(4), both neonatal and subsequent); Asian ancestry (higher cord TSH); male sex (higher TSH and lower neonatal bloodspot total T(4)); and C-section (lower cord TSH). Gestational age was independently associated with lower cord TSH, higher cord total T(4), and higher neonatal and subsequent bloodspot total T(4). CONCLUSIONS Fetal and newborn thyroid hormone levels during the perinatal period are dynamic and influenced by several biological and delivery related factors. Efforts to identify fetal thyroid disruptors in late gestation must carefully consider these factors.
From Quellung to Multiplex PCR, and Back When Needed, in Pneumococcal Serotyping

ABSTRACT All currently available vaccines against Streptococcus pneumoniae are based on selections of the over 90 different serotypes, which underlines the importance of serotyping for surveillance and vaccine efficacy monitoring. In this study, we modified and validated a PCR-based scheme for deducing the serotypes of the invasive pneumococci isolated in Finland. For validation, 170 isolates were serotyped using the new protocol with six sequential multiplex PCRs for the deduction of serotypes, supplemented with Quellung testing when needed. The results were compared with those obtained by traditional serotyping methods. We found that 98.8% (168/170) of the isolates were correctly serotyped by the new protocol. Subsequently, the scheme was taken into regular use for serotyping the invasive pneumococci isolated in Finland for serotype-specific surveillance purposes and has been applied in the serotyping of more than 1,500 invasive isolates so far. The sequential multiplex PCRs (mPCRs) have given a result for over 99% of the isolates and allowed us to both handle samples in bulk and noticeably reduce the cost of reagents. While serotyping primarily by PCR is precise and effective, Quellung testing remains the most reliable way to discover possible discrepancies between the DNA deduced and the phenotypic serotype of an isolate. Since implementing the protocol for regular use, two serotype 19F PCR-positive isolates were found to be serotype 19A by the Quellung reaction. While a rare occurrence, this is an important observation, which prompted a revision of our serotyping protocol to prevent possible underreporting of serotype 19A, a potential replacement serotype following large-scale vaccination.
[Optic nerve head parameters as measured by confocal scanning laser (Heidelberg Retina Tomograph II) in normal, ocular hypertensive and glaucomatous subjects].

PURPOSE To compare the optic nerve parameters measured by confocal scanning laser in normal, ocular hypertensive and glaucomatous eyes; and in groups of ocular hypertensive eyes, classification of these according to the optic nerve appearance and to short-wavelength automated perimetry (SWAP) results. METHODS 101 eyes of 101 normal subjects, 247 eyes of 247 ocular hypertensive subjects and 102 eyes of 102 glaucomatous subjects were studied. Subjects were classified based on intraocular pressure and standard automated perimetry (AP) performance. Hypertensive subjects were classified into ocular hypertensive and preperimetric glaucoma, and into ocular hypertensive with normal SWAP and hypertensive with pathological SWAP findings. Every patient underwent evaluation of the optic nerve, AP, SWAP and confocal scanning laser ophthalmoscopy (HRT II), resulting in the acquisition of topographic parameters of the optic nerve, which were then compared between the different groups. RESULTS Significant differences (p<0.05) were found between normal subjects and glaucomatous eyes in all optic nerve parameters except disc area (2.23/2.1), height variation contour (0.41/0.39) and average variability (0.05/0.04). Ocular hypertensive eyes showed an overlap when compared with normal and glaucoma groups. No differences were found between normal subjects and those with ocular hypertension in mean retinal nerve fiber layer thickness (0.24/0.24) or between those with ocular hypertension and glaucoma in mean cup depth (0.28/0.3). Nevertheless, when those with ocular hypertension were segregated based on clinical evaluation of optic nerve or SWAP performance, the ability to define the presence of structural glaucoma damage improved significantly. CONCLUSIONS HRT enables moderate discrimination between normal, ocular hypertensive and glaucoma subjects. The use of diagnostic tests to detect early glaucomatous damage (such as short-wavelength automated perimetry) in ocular hypertensive eyes improves the ability of HRT to discriminate glaucoma.
Ring1b-mediated H2A Ubiquitination Associates with Inactive X Chromosomes and Is Involved in Initiation of X Inactivation*

Histone modifications are thought to serve as epigenetic markers that mediate dynamic changes in chromatin structure and regulation of gene expression. As a model system for understanding epigenetic silencing, X chromosome inactivation has been previously linked to a number of histone modifications including methylation and hypoacetylation. In this study, we provide evidence that supports H2A ubiquitination as a novel epigenetic marker for the inactive X chromosome (Xi) and links H2A ubiquitination to initiation of X inactivation. We found that the H2A-K119 ubiquitin E3 ligase Ring1b, a Polycomb group protein, is enriched on Xi in female trophoblast stem (TS) cells as well as differentiating embryonic stem (ES) cells. Consistent with Ring1b mediating H2A ubiquitination, ubiquitinated H2A (ubH2A) is also enriched on the Xi of both TS and ES cells. We demonstrate that the enrichment of Ring1b and ubH2A on Xi is transient during TS and ES cell differentiation, suggesting that the Ring1b and ubH2A are involved in the initiation of both imprinted and random X inactivation. Furthermore, we showed that the association of Ring1b and ubH2A with Xi is mitotically stable in non-differentiated TS cells.
Assessing Community Change at Multiple Levels: The Genesis of an Evaluation Framework for the California Healthy Cities Project

More than 40 cities have participated in the California Healthy Cities Project since its inception in 1988. Because Healthy Cities efforts are community driven, these cities address diverse health and social issues using a wide variety of strategies. This complexity, in addition to the usual difficulties associated with evaluating community interventions, creates many challenges for evaluation. Given the community building and process orientation of Healthy Cities, it may be most appropriate to measure intermediate community changes that have been linked to health outcomes in previous research or, at a minimum, theoretically. The California Healthy Cities evaluation framework conceptualizes change at five levels: individual, civic participation, organizational, interorganizational, and community. The framework, developed collaboratively with Healthy Cities participants, attempts to synthesize current thinking and practice on evaluation of community projects by applying concepts from community capacity/competence, social ecology, and urban planning.
[Bronchoscopic removal of foreign body from airway through tracheotomy or tracheostomy].

OBJECTIVE Most foreign bodies in the airway are removed by respiratory endoscopy. Rarely, the removal of the foreign body has to be performed through endoscopic control by tracheotomy or tracheostomy. This article reports three cases of foreign body removal in children performed by tracheal opening. DESCRIPTION Retrospective review of records with report of three cases of children who aspirated foreign bodies into the airway. In the first case, there was rupture of the tracheostomy tube, with aspiration of its distal portion. Endoscopic removal was performed by tracheostomy. The second child aspirated a pen cap. It could not be removed by endoscopy because it would not pass through the subglottic region. Cervical tracheotomy was performed and the foreign body was removed with endoscopic control. In the last case, the foreign body was in the left main bronchus. It was removed by bronchoscopy through tracheostomy opening. All children presented good outcome after the endoscopic procedure. The trachea of the patient submitted to tracheotomy was sutured after the foreign body removal. Tracheostomy was not necessary. In the children with previous tracheostomy, the tube was put back after the foreign body removal. COMMENTS Most foreign bodies in the airway of children can be removed by endoscopy. When the foreign body is too large to pass through the subglottic region, or so sharp that it can injure the airway, the use of tracheotomy or tracheostomy is indicated.
Synergistic Interactions of Vancomycin with Different Antibiotics against Escherichia coli: Trimethoprim and Nitrofurantoin Display Strong Synergies with Vancomycin against Wild-Type E. coli

ABSTRACT Gram-negative bacteria are normally resistant to the antibiotic vancomycin (VAN), which cannot significantly penetrate the outer membrane. We used Escherichia coli mutants that are partially sensitive to VAN to study synergies between VAN and 10 other antibiotics representing six different functional categories. We detected strong synergies with VAN and nitrofurantoin (NTR) and with VAN and trimethoprim (TMP) and moderate synergies with other drugs, such as aminoglycosides. These synergies are powerful enough to show the activity of VAN against wild-type E. coli at concentrations of VAN as low as 6.25 μg/ml. This suggests that a very small percentage of exogenous VAN does enter E. coli but normally has insignificant effects on growth inhibition or cell killing. We used the results of pairwise interactions with VAN and the other 10 antibiotics tested to place VAN into a functional category of its own, as previously defined by Yeh et al. (P. Yeh, A. I. Tschumi, and R. Kishony, Nat Genet 28:489–494, 2006, http://dx.doi.org/10.1038/ng1755).
Sequence analysis of the 17-kilodalton-antigen gene from Rickettsia rickettsii

DNA obtained from the Sheila Smith strain of Rickettsia rickettsii was digested to completion with the restriction endonucleases BamHI and SalI and ligated with the plasmid vector pUC19. The ligation mixture was used to transform Escherichia coli. A total of 465 bacterial clones were screened for antigen production with hyperimmune rabbit serum. One of the reactive clones, containing a recombinant plasmid designated pSS124, was solubilized and subjected to immunoblot analysis and revealed expression of a 17-kilodalton protein reactive with anti-R. rickettsii serum that comigrated with an antigen from R. rickettsii. A 1.6-kilobase PstI-BamHI fragment from pSS124 was subcloned and continued to direct synthesis of the 17-kilodalton antigen. The nucleotide sequence was determined for this 1.6-kilobase subclone, which encompassed the gene encoding the polypeptide as well as flanking regions containing potential regulatory sequences. The open reading frame consisted of 477 nucleotides that specified a 159-amino-acid protein with a calculated molecular weight of 16,840. The deduced amino acid sequence contained a hydrophobic sequence near the amino terminus that resembled signal peptides described for E. coli. The carboxy terminus was hydrophilic in nature and probably contained the exposed epitopes.
Evidence for a Renomedullary Vasodepressor System in Rabbits and Dogs

Renal perfusion was increased in anesthetized rabbits and dogs by using an extracorporeal circuit. When left kidney perfusion pressure was raised in rabbits (145-240 mm Hg), arterial pressure fell by 1 J4±0J0 mm Hg/min. Pretreatment of the rabbits with 2-bromoethylamine hydrobromide, which destroyed the renal medulla, abolished the fall in arterial pressure (-0.08 ±0.08 mm Hg/min) in response to increased renal perfusion pressure. In dogs (with blockade of autonomic ganglia by pentolinium, converting enzyme inhibition [captopril/ enalaprilat], and surgical renal denervation), increasing renal perfusion pressure to 170-220 mm Hg resulted in a fall in arterial pressure by 0.32±0.03 mm Hg/min (or by 28.9±3.1 mm Hg over a 90-minute period). Mean arterial pressure did not change significantly in identically prepared dogs not subjected to increased renal perfusion pressure, whereas pretreatment of dogs with bromoethylamine abolished the hypotensive response to increased renal perfusion pressure. Thus, the hypotensive response to increased renal perfusion was dependent on the presence of an intact renal medulla, but hypotension still occurred in the presence of converting enzyme inhibition, autonomic ganglion blockade, and renal denervation. The results provide in vivo evidence in two species that a vasodepressor factor from the renal medulla is released in response to increased renal perfusion.
Smoking Cessation and Chronic Pain: Patient and Pain Medicine Physician Attitudes

Although previous studies suggest that the clinical setting of an interdisciplinary pain treatment program may provide an optimal environment to promote smoking cessation, currently available smoking cessation interventions may be less effective for adults with chronic pain due, in part, to unrecognized clinical factors related to chronic pain. The specific aim of this qualitative study was to solicit information from adult smokers with chronic pain participating in an interdisciplinary pain treatment program regarding their perceptions of how smoking affects pain symptoms, and how these beliefs, cognitions, and emotions may either impede or facilitate smoking cessation. Similar information was solicited from a group of pain specialty physicians. The study involved 18 smokers with chronic pain, and seven physicians. Patients reported that smoking was an important coping strategy for pain and distress, primarily by offering an opportunity for distraction and avoidance, respectively. The majority of patients using opioids reported that opioid consumption stimulated smoking. Important barriers were identified toward making a quit attempt during pain treatment including quitting smoking while making changes in opioid use, and perceived difficulty managing multiple treatment‐related stressors. Several pain‐related benefits of smoking cessation were identified by physicians, but important barriers to providing smoking cessation services were recognized including lack of time and knowledge about how to help patients quit smoking. The findings of this study identified several novel and important clinical factors that should be incorporated into a targeted smoking cessation intervention for adults with chronic pain.