Miracle-dz/UniFAR-FTUs huggingface dataset:
GATA4, 5 and 6 mediate TGFβ maintenance of endodermal gene expression in Xenopus embryos

The individual contributions of the three vertebrate GATA factors to endoderm formation have been unclear. Here we detail the early expression of GATA4, 5 and 6 in presumptive endoderm in Xenopus embryos and their induction of endodermal markers in presumptive ectoderm. Induction of HNF3β by all three GATA factors was abolished when protein synthesis was inhibited, showing that these inductions are indirect. In contrast, whereas induction of Sox17α and HNF1β by GATA4 and 5 was substantially reduced when protein synthesis was inhibited, induction by GATA6 was minimally affected, suggesting that GATA6 is a direct activator of these early endodermal genes. GATA4 induced GATA6 expression in the same assay and antisense morpholino oligonucleotides (MOs), designed to knock down translation of GATA6, blocked induction of Sox17α and HNF1β by GATA4, suggesting that GATA4 induces these genes via GATA6 in this assay. All three GATA factors were induced by activin, although GATA4 and 6 required lower concentrations. GATA MOs inhibited Sox17α and HNF1β induction by activin at low and high concentrations in the order: GATA6>GATA4>GATA5. Together with the timing of their expression and the effects of GATA MOs in vivo, these observations identify GATA6 as the predominant GATA factor in the maintenance of endodermal gene expression by TGFβ signaling in gastrulating embryos. In addition, examination of gene expression and morphology in later embryos, revealed GATA5 and 6 as the most critical for the development of the gut and the liver.
In vitro and in vivo imaging of initial B-T-cell interactions in the setting of B-cell based cancer immunotherapy

There has been a growing interest in the use of B cells for cancer vaccines, since they have yielded promising results in preclinical animal models. Contrary to dendritic cells (DCs), we know little about the migration behavior of B cells in vivo. Therefore, we investigated the interactions between CD40-activated B (CD40B) cells and cytotoxic T cells in vitro and the migration behavior of CD40B cells in vivo. Dynamic interactions of human antigen-presenting cells (APCs) and T cells were observed by time-lapse video microscopy. The migratory and chemoattractant potential of CD40B cells was analyzed in vitro and in vivo using flow cytometry, standard transwell migration assays, and imaging of fluorescently labeled murine CD40B cells. Murine CD40B cells show migratory features similar to human CD40B cells. They express important lymph node homing receptors which were functional and induced chemotaxis of T cells in vitro. Striking differences were observed with regard to interactions of human APCs with T cells. CD40B cells differ from DCs by displaying a rapid migratory pattern undergoing highly dynamic, short-lived and sequential interactions with T cells. In vivo, CD40B cells are home to the secondary lymphoid organs where they accumulate in the B cell zone before traveling to the B/T cell boundary. Moreover, intravenous (i.v.) administration of murine CD40B cells induced an antigen-specific cytotoxic T cell response. Taken together, this data show that CD40B cells home secondary lymphoid organs where they physically interact with T cells to induce antigen-specific T cell responses, thus underscoring their potential as cellular adjuvant for cancer immunotherapy.
Efficacy of neutral and negatively charged liposome-loaded gentamicin on planktonic bacteria and biofilm communities

We investigated the efficacy of liposomal gentamicin formulations of different surface charges against Pseudomonas aeruginosa and Klebsiella oxytoca. The liposomal gentamicin formulations were prepared by the dehydration–rehydration method, and their sizes and zeta potential were measured. Gentamicin encapsulation efficiency inside the liposomal formulations was determined by microbiologic assay, and stability of the formulations in biologic fluid was evaluated for a period of 48 h. The minimum inhibitory concentration and the minimum bactericidal concentration were determined, and the in vitro time kill studies of the free form of gentamicin and liposomal gentamicin formulations were performed. The activities of liposomal gentamicin in preventing and reducing biofilm-forming P. aeruginosa and K. oxytoca were compared to those of free antibiotic. The sizes of the liposomal formulations ranged from 625 to 806.6 nm in diameter, with the zeta potential ranging from −0.22 to −31.7 mV. Gentamicin encapsulation efficiency inside the liposomal formulation ranged from 1.8% to 43.6%. The liposomes retained >60% of their gentamicin content during the 48 h time period. The minimum inhibitory concentration of neutral formulation was lower than that of free gentamicin (0.25 versus 1 mg/L for P. aeruginosa and 0.5 versus 1 mg/L for K. oxytoca). The negatively charged formulation exhibited the same bacteriostatic concentration as that of free gentamicin. The minimum bactericidal concentration of neutral liposomes on planktonic bacterial culture was twofold lower than that of free gentamicin, whereas the negatively charged formulations were comparable to free gentamicin. The killing time curve values for the neutral negatively charged formulation against planktonic P. aeruginosa and K. oxytoca were better than those of free gentamicin. Furthermore, liposomal formulations prevent the biofilm-formation ability of these strains better than free gentamicin. In summary, liposomal formulations could be an effective lipid nanoparticle to combat acute infections where planktonic bacteria are predominant.
Type III secretion translocation pores of Yersinia enterocolitica trigger maturation and release of pro‐inflammatory IL‐1β

Bacteria from the genus Yersinia deliver a number of effectors into host cells via type III secretion (T3S). Injected Yop effectors interfere and prevent pro‐inflammatory warning signals by hijacking the host's intracellular machinery. While macrophages infected by wild‐type Yersinia enterocolitica did not release mature IL‐1β, macrophages infected by Y. enterocolitica deprived of all effectors released mature IL‐1β. Surprisingly, macrophages infected by Y. enterocolitica deficient for secretion of all T3S proteins, including effectors and translocators, did not release mature IL‐1β. Using different genetic constructs, we show that insertion of T3S translocation pores trigger activation of caspase‐1, maturation of proIL‐1β and release of mature IL‐1β, which occurs independently of cell osmotic lysis. These data show that T3S translocation is intrinsically a pro‐inflammatory phenomenon. However, in the case of Yersinia, this effect is neutralized by the action of effectors.
Patterns of Antimicrobial Resistance Among Intensive Care Unit Patients of A Private Medical College Hospital in Dhaka

Because of importance of Hospital acquired infections (HAIs), it is critical to conduct surveillance studies to obtain the required data about the regional microorganisms and their susceptibility to antibiotics. This study to investigate antimicrobial resistance pattern among Intensive Care Unit (ICU) patients in a private medical college hospital setup. In a cross sectional study, 100 specimens from patients admitted in the ICU who had signs or symptoms of nosocomial infection were collected from 2012 - 2013. For each patient, samples of blood, urine, tracheal aspirate, sputum, wound swab, pus, and endotracheal tubes were obtained, cultured and analyzed with antibiogram. The most common primary diagnosis were aspiration pneumonia (49%) and UTI (20%) respectively. The most common locations for infection were tracheal aspirate (54%). The most frequent gram negative microorganisms derived from samples were Acinetobacter spp (29%), Klebsiella spp (26%) and Pseudomonas spp (18%). Klebsiella spp, Acinetobacter spp and Pseudomonas spp were most common resistant organisms among all. Klebsiella spp were resistant against Ceftriaxone (84.6%), Ceftazidime (82.6%), Amikacin (46.1%), Gentamicin (66.6%) and Quinolones (65-66.6%) respectively. Acinetobacter spp were resistant against Ceftriaxone (85%), Ceftazidime (88.8%), Cefotaxime (85.7%), Meropenem (79.3%),Amikacin (86.2%), Gentamicin (84.5%) and Quinolons (86.2-89.2%) respectively. Pseudomonas spp were resistant against Ceftriaxone (70.5%), Ceftazidime (66.6%), Amikacin (68.7%), Gentamicin (58.8%), Meropenem (52.9%) and Quinolones (81.2-86.6%) respectively. Meropenem was the most sensitive antibiotic against Klebsiella spp (84.6%) but Cotrimoxazole in case of Acinetobacter spp (60%) respectively. Escherichia coli were mostly isolated from urine, which was sensitive to Amikacin (73.3%) and Meropenem (86.6%) respectively. Gram-negative pathogens obtained from ICU patients in our settings show high resistance to antibiotics. Regular monitoring of the pattern of resistance of common pathogens in the ICUs is essential to up-to-date the use of rational antibiotics regiments. Bangladesh J Medicine Jul 2014; 25 (2) : 47-51
Free turbulent shear layer in a point vortex gas as a problem in nonequilibrium statistical mechanics.

This paper attempts to unravel any relations that may exist between turbulent shear flows and statistical mechanics through a detailed numerical investigation in the simplest case where both can be well defined. The flow considered for the purpose is the two-dimensional (2D) temporal free shear layer with a velocity difference ΔU across it, statistically homogeneous in the streamwise direction (x) and evolving from a plane vortex sheet in the direction normal to it (y) in a periodic-in-x domain L×±∞. Extensive computer simulations of the flow are carried out through appropriate initial-value problems for a "vortex gas" comprising N point vortices of the same strength (γ=LΔU/N) and sign. Such a vortex gas is known to provide weak solutions of the Euler equation. More than ten different initial-condition classes are investigated using simulations involving up to 32000 vortices, with ensemble averages evaluated over up to 103 realizations and integration over 104L/ΔU. The temporal evolution of such a system is found to exhibit three distinct regimes. In Regime I the evolution is strongly influenced by the initial condition, sometimes lasting a significant fraction of L/ΔU. Regime III is a long-time domain-dependent evolution towards a statistically stationary state, via "violent" and "slow" relaxations [ P.-H. Chavanis Physica A 391 3657 (2012)], over flow time scales of order 102 and 104L/ΔU, respectively (for N=400). The final state involves a single structure that stochastically samples the domain, possibly constituting a "relative equilibrium. " The vortex distribution within the structure follows a nonisotropic truncated form of the Lundgren-Pointin (L-P) equilibrium distribution (with negatively high temperatures; L-P parameter λ close to -1). The central finding is that, in the intermediate Regime II, the spreading rate of the layer is universal over the wide range of cases considered here. The value (in terms of momentum thickness) is 0.0166±0.0002 times ΔU. Regime II, extensively studied in the turbulent shear flow literature as a self-similar "equilibrium" state, is, however, a part of the rapid nonequilibrium evolution of the vortex-gas system, which we term "explosive" as it lasts less than one L/ΔU. Regime II also exhibits significant values of N-independent two-vortex correlations, indicating that current kinetic theories that neglect correlations or consider them as O(1/N) cannot describe this regime. The evolution of the layer thickness in present simulations in Regimes I and II agree with the experimental observations of spatially evolving (3D Navier-Stokes) shear layers. Further, the vorticity-stream-function relations in Regime III are close to those computed in 2D Navier-Stokes temporal shear layers [ J. Sommeria, C. Staquet and R. Robert J. Fluid Mech. 233 661 (1991)]. These findings suggest the dominance of what may be called the Kelvin-Biot-Savart mechanism in determining the growth of the free shear layer through large-scale momentum and vorticity dispersal.
Recovery from coma caused by primary CNS mantle cell lymphoma presenting as encephalitis

We report a 74-year-old woman with progressive cognitial deterioration and changes in personality. She had no clinical signs of an inflammatory CNS process, but brain CT and MRI scans and cytologic examination of the CSF were initially indicative of encephalitis and ventriculitis. Antiviral and antibacterial therapy had no effect on the course of symptoms, and patient became comatose. We established the diagnosis of a primary CNS mantle cell lymphoma (PCNSL) and began corticosteroids. Within a few days the patient became alert and was able to walk again. Nonenhancing and non-space-occupying PCNSLs are rare but must be considered in the differential diagnosis of coma and encephalitis. Comatose PCNSL patients without radiographic evidence for herniation can be successfully treated with corticosteroids even if the EEG has a burst suppression pattern.
Heart rate variability in patients with iron deficiency anemia.

BACKGROUND Heart rate variability (HRV) is associated with increased cardiac risk factor in several conditions. The iron status of an individual may play an important role in cardiovascular health. OBJECTIVE To evaluate heart rate variability in patients with iron deficiency anemia. METHODS Twenty-three patients with iron deficiency anemia (mean hemoglobin (Hb) 8.6+/-2.2 g/dl) and 10 healthy people (mean Hb 13.9+/-1.2 g/dl) were assessed with 24-hour ambulatory Holter recordings during in hospital course having limited physical activity. RESULTS Although mean heart rate was significantly higher in patients with anemia, there was no significant difference regarding HRV parameters compared to the healthy group. CONCLUSION There was no significant difference in HRV parameters between patients with iron deficiency anemia with limited physical activity and healthy ambulatory people.
Adherent bacterial colonization in the pathogenesis of osteomyelitis

Osteomyelitic bone can be plagued by extensive bacterial growth in adherent biofilms, which can be observed by direct scanning electron microscropy, and may even obscure the entire infected bone surface. Through synchronized production of exopolysaccharide polymers, microcolony formation and surface adhesion is mediated, and a fibrous matrix is formed which is readily visible by transmission electron microscopy. Multiple bacterial morphotypes may be present simultaneously in these biofilms. The result is an infection that may be very resistant to either antibiotic therapy or host clearance in the damaged tissue or bone, leading to persistent infection unless the compromised material is removed.
Dynamic Canal Encroachment of Ligamentum Flavum: An In Vitro Study of Cadaveric Specimens

Objective In extension of the cervical spine, the ligamentum flavum (LF) may bulge and intrude into the vertebral canal and cause symptoms of myelopathy and/or radiculopathy in patients with canal stenosis. Knowledge of the relationship between the extension angle and the physiologic changes of the LF is important for a better understanding of the clinical symptoms. The current study was designed to demonstrate the dynamic correlativity of canal intrusion of the LF bulge with the extension angle of the cervical spine. Methods With a novel method, the probe of the electrical resistance strain gauge was put into the cervical canals of 14 cadaveric specimens. The LF bulge distance of six segments (C2–C3 to C7–T1) and corresponding extension angles of every 5° from 0° to 45° were collected. Angle–bulge curves were drawn. Results In overextension (45°), C5–C6 had the biggest canal intrusion depth (3.478±0.527 mm), whereas the upper and lower segments declined gradually (C5–C6>C4–C5>C6–C7>C3–C4>C7–T1>C2–C3). The curves in all segments were sigmoidal, which demonstrated the dynamic change of LF, that is, during the process of extension, LF shortened and contracted first, after the original length was reached, it began to bulge and burst into the canal. Conclusion The current study has provided a method to measure inner canal kinematic changes in intact spinal specimens.
Trends in Catheter-Associated Urinary Tract Infections in Adult Intensive Care Units—United States, 1990–2007

Background. Over the past 2 decades, multiple interventions have been developed to prevent catheter-associated urinary tract infections (CAUTIs). The CAUTI prevention guidelines of the Healthcare Infection Control Practices Advisory Committee were recently revised. Objective. To examine changes in rates of CAUTI events in adult intensive care units (ICUs) in the United States from 1990 through 2007. Methods. Data were reported to the Centers for Disease Control and Prevention (CDC) through the National Nosocomial Infections Surveillance System from 1990 through 2004 and the National Healthcare Safety Network from 2006 through 2007. Infection preventionists in participating hospitals used standard methods to identify all CAUTI events (categorized as symptomatic urinary tract infection [SUTI] or asymptomatic bacteriuria [ASB]) and urinary catheter–days (UC-days) in months selected for surveillance. Data from all facilities were aggregated to calculate pooled mean annual SUTI and ASB rates (in events per 1,000 UC-days) by ICU type. Poisson regression was used to estimate percent changes in rates over time. Results. Overall, 36,282 SUTIs and 22,973 ASB episodes were reported from 367 facilities representing 1,223 adult ICUs, including combined medical/surgical (505), medical (212), surgical (224), coronary (173), and cardiothoracic (109) ICUs. All ICU types experienced significant declines of 19%–67% in SUTI rates and 29%–72% in ASB rates from 1990 through 2007. Between 2000 and 2007, significant reductions in SUTI rates occurred in all ICU types except cardiothoracic ICUs. Conclusions. Since 1990, CAUTI rates have declined significantly in all major adult ICU types in facilities reporting to the CDC. Further efforts are needed to assess prevention strategies that might have led to these decreases and to implement new CAUTI prevention guidelines.
Divergent effects of oncostatin M on astroglioma cells: Influence on cell proliferation, invasion, and expression of matrix metalloproteinases

Oncostatin M (OSM), a cytokine of the interleukin‐6 (IL‐6) family, can either promote or inhibit cell growth in various normal and tumor cells. We addressed the effects of exogenous OSM on the proliferation and invasion of human astroglioma cells. In addition, we investigated one of the possible mechanisms involved: modulation of matrix metalloproteinase (MMP) expression and enzymatic activity. We found that OSM inhibited the proliferation of two human astroglioma cell lines (CH235‐MG and U87‐MG), and that this effect was not due to apoptosis. The inhibitory effect of OSM on proliferation was mediated through the gp130/OSMRβ receptor complex. To extend these findings, we analyzed the effects of OSM on primary tumor cells from glioblastoma patients. OSM suppressed the proliferation of primary glioblastoma cells, but not that of normal astrocytes. Interestingly, OSM did not suppress astroglioma cell invasion. This may be due to the differential regulation of MMPs by OSM. We found that OSM inhibited the constitutive expression of MMP‐2, while MMP‐9 expression was enhanced in astroglioma cell lines. We conclude that OSM inhibits proliferation of human astroglioma cells and primary glioblastoma cells via the gp130/OSMRβ receptor complex. However, OSM does not affect the invasive capacity of the astroglioma cells, which may be due to the divergent effects of OSM on MMP‐2 and MMP‐9 expression. Collectively, these findings suggest a complex role for OSM in astroglioma biology. © 2005 Wiley‐Liss, Inc.
Treatment of hepatic venous outflow obstruction after piggyback liver transplantation.

PURPOSE To evaluate retrospectively the endovascular management of hepatic venous outflow obstruction after piggyback orthotopic liver transplantation. MATERIALS AND METHODS The study was performed with the approval and under the guidelines of the institutional review board and complied with the Health Insurance Portability and Accountability Act. Informed consent from patients was not required by the institutional review board for this retrospective study. From 1995 to 2003, 13 patients (eight male, five female), including 12 adults and one adolescent (age range, 14-67 years; median age, 52 years), underwent endovascular treatment of hepatic venous outflow obstruction after piggyback orthotopic liver transplantation. Patients gave informed consent for all procedures. Eleven patients received whole livers, and two received living-related donor right liver lobes. Four underwent repeat piggyback orthotopic liver transplantation prior to intervention. Primary stent placement was performed in 12 patients. One patient refused primary stent placement and chose venoplasty alone, but required a stent 5 months later. Short balloon-expandable stents (mean diameter, 14.6 mm +/- 1.1 [standard deviation]) were used to minimize jailing of branch vessels and to resist recoil. Pre- and post-procedural pressure gradients were measured. Follow-up included venography, cross-sectional imaging, and laboratory tests. The Wilcoxon signed rank test or the sign test was performed to compare pre- and post-procedural pressure gradients, body weights, and laboratory values. RESULTS Technical success (pressure gradient < or = 3 mm Hg) was achieved in 13 of 13 patients, and clinical success, in 12 of 13. Mean pre- and post-procedural pressure gradients were 13.0 mm Hg +/- 1.4 and 0.8 mm Hg +/- 0.3. Mean interval from transplantation to intervention was 348 days +/- 159. Mean follow-up was 678 days (range, 16-2880 days). Technical success did not result in clinical improvement in one patient. Biopsy demonstrated severe hepatic necrosis, likely from prolonged venous congestion, and the patient required repeat transplantation. Only one patient required reintervention for stent migration, and no other complications occurred. No significant restenosis was encountered after stent placement. CONCLUSION Hepatic venous outflow obstruction is an uncommon but potentially fatal complication of piggyback orthotopic liver transplantation. Endovascular treatment with balloon-expandable stents is effective, safe, and apparently durable.
Enumeration and isolation of cellulolytic and hemicellulolytic bacteria from human feces

The fibrolytic microbiota of the human large intestine was examined to determine the numbers and types of cellulolytic and hemicellulolytic bacteria present. Fecal samples from each of five individuals contained bacteria capable of degrading the hydrated cellulose in spinach and in wheat straw pretreated with alkaline hydrogen peroxide (AHP-WS), whereas degradation of the relatively crystalline cellulose in Whatman no. 1 filter paper (PMC) was detected for only one of the five samples. The mean concentration of cellulolytic bacteria, estimated with AHP-WS as a substrate, was 1.2 X 10(8)/ml of feces. Pure cultures of bacteria isolated on AHP-WS were able to degrade PMC, indicating that interactions with other microbes were primarily responsible for previous low success rates in detecting fecal cellulolytic bacteria with PMC as a substrate. The cellulolytic bacteria included Ruminococcus spp. , Clostridium sp. , and two unidentified strains. The mean concentration of hemicellulolytic bacteria, estimated with larchwood xylan as a substrate, was 1.8 X 10(10)/ml of feces. The hemicellulose-degrading bacteria included Butyrivibrio sp. , Clostridium sp. , Bacteroides sp. , and two unidentified strains, as well as four of the five cellulolytic strains. This work demonstrates that many humans harbor intestinal cellulolytic bacteria and that a hydrated cellulose source such as AHP-WS is necessary for their consistent detection and isolation.