Miracle-dz/UniFAR-FTUs huggingface dataset:
Protease homolog BepA (YfgC) promotes assembly and degradation of β-barrel membrane proteins in Escherichia coli

Significance Outer membrane proteins (OMPs) are involved in important cellular activities in Gram-negative bacteria. Although the bepA (formerly yfgC) gene encoding a putative metalloprotease has been implicated in quality control of OMPs, its specific function remains unclear. This study reveals that BepA promotes assembly of LptD, an OMP involved in the transport of lipopolysaccharides, which undergoes intramolecular disulfide rearrangement during its biogenesis. BepA also promotes degradation of incorrectly folded LptD. BamA, another OMP involved in OMP assembly, is also degraded in a BepA-dependent manner in the absence of periplasmic chaperone SurA. BepA thus controls the quality of OMPs by promoting either the biogenesis or elimination of OMPs, depending on their folding state. Gram-negative bacteria are equipped with quality-control systems for the outer membrane (OM) that sense and cope with defective biogenesis of its components. Accumulation of misfolded outer membrane proteins (OMPs) in Escherichia coli leads to activation of σE, an essential alternative σ factor that up-regulates transcription of multiple genes required to preserve OM structure and function. Disruption of bepA (formerly yfgC), a σE-regulated gene encoding a putative periplasmic metalloprotease, sensitizes cells to multiple drugs, suggesting that it may be involved in maintaining OM integrity. However, the specific function of BepA remains unclear. Here, we show that BepA enhances biogenesis of LptD, an essential OMP involved in OM transport and assembly of lipopolysaccharide, by promoting rearrangement of intramolecular disulfide bonds of LptD. In addition, BepA possesses protease activity and is responsible for the degradation of incorrectly folded LptD. In the absence of periplasmic chaperone SurA, BepA also promotes degradation of BamA, the central OMP subunit of the β-barrel assembly machinery (BAM) complex. Interestingly, defective oxidative folding of LptD caused by bepA disruption was partially suppressed by expression of protease-active site mutants of BepA, suggesting that BepA functions independently of its protease activity. We also show that BepA has genetic and physical interaction with components of the BAM complex. These findings raised the possibility that BepA maintains the integrity of OM both by promoting assembly of OMPs and by proteolytically eliminating OMPs when their correct assembly was compromised.
The deoxynucleotide triphosphohydrolase SAMHD1 is a major regulator of DNA precursor pools in mammalian cells

Sterile alpha motif and HD-domain containing protein 1 (SAMHD1) is a triphosphohydrolase converting deoxynucleoside triphosphates (dNTPs) to deoxynucleosides. The enzyme was recently identified as a component of the human innate immune system that restricts HIV-1 infection by removing dNTPs required for viral DNA synthesis. SAMHD1 has deep evolutionary roots and is ubiquitous in human organs. Here we identify a general function of SAMHD1 in the regulation of dNTP pools in cultured human cells. The protein was nuclear and variably expressed during the cell cycle, maximally during quiescence and minimally during S-phase. Treatment of lung or skin fibroblasts with specific siRNAs resulted in the disappearence of SAMHD1 accompanied by loss of the cell-cycle regulation of dNTP pool sizes and dNTP imbalance. Cells accumulated in G1 phase with oversized pools and stopped growing. Following removal of the siRNA, the pools were normalized and cell growth restarted, but only after SAMHD1 had reappeared. In quiescent cultures SAMHD1 down-regulation leads to a marked expansion of dNTP pools. In all cases the largest effect was on dGTP, the preferred substrate of SAMHD1. Ribonucleotide reductase, responsible for the de novo synthesis of dNTPs, is a cytosolic enzyme maximally induced in S-phase cells. Thus, in mammalian cells the cell cycle regulation of the two main enzymes controlling dNTP pool sizes is adjusted to the requirements of DNA replication. Synthesis by the reductase peaks during S-phase, and catabolism by SAMHD1 is maximal during G1 phase when large dNTP pools would prevent cells from preparing for a new round of DNA replication.
Early Childhood Masturbation: A Clinical Study

Objectives: To study the characteristics of masturbation in children below the age of six years and to assess the course and outcome of this condition. Methods and Materials: A retrospective study of all children diagnosed to have masturbation at the pediatric clinic of Queen Alia Military Hospital over duration of three and half year’s period. A data- collecting sheet was developed which includes information on demographic characteristics, clinical presentations, investigations and modes of treatment. Children with proven urinary tract infection, epilepsy and gastrointestinal disease were excluded from our study. Results: Fifteen children (6 males and 9 females) were found to have masturbation during the study period. The most common reason for presentation to the clinic was possible urinary tract infection (8=53.3%), abdominal pain (4=26.7%) and possible epileptic seizures (3=20%). The age at first symptom was variable with a mean of 18.5 months. The frequency of the masturbation act varied from 3 times per week to 10 times per day. Only one child had abnormal EEG, four children had extensive investigations. Only one child aged 10 months had home video recording. Twelve patients were treated with behavioral therapy alone. Three female children had in addition to behavioral therapy, local Zylocaine cream at the genital area. Conclusion: Masturbation is not uncommon in young children and should be included in the differential diagnosis of common pediatric instinct. Home video recording of events may prevent unnecessary investigations and treatments.
Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

Significance Recent single-cell studies showed that gene transcription in mammals is fundamentally stochastic, occurring in short and intense transcriptional bursts. However, less is known on how transcriptional bursting is modulated upon stimulation. Here, we monitor the transcriptional response of a single allele of the endogenous connective tissue growth factor gene, encoding a secreted protein involved in wound healing and response to shear stress, to two different physiological stimuli in single cells. Analysis using stochastic modeling shows that both stimuli cause acute transcriptional responses characterized by transiently modified gene activities, and increased transcription rates that may last longer depending on the stimulus. These results provide insights on how transcriptional bursting kinetics can be adjusted to increase gene expression upon physiological stimulations. Mammalian genes are often transcribed discontinuously as short bursts of RNA synthesis followed by longer silent periods. However, how these “on” and “off” transitions, together with the burst sizes, are modulated in single cells to increase gene expression upon stimulation is poorly characterized. By combining single-cell time-lapse luminescence imaging with stochastic modeling of the time traces, we quantified the transcriptional responses of the endogenous connective tissue growth factor gene to different physiological stimuli: serum and TGF-β1. Both stimuli caused a rapid and acute increase in burst sizes. Whereas TGF-β1 showed prolonged transcriptional activation mediated by an increase of transcription rate, serum stimulation resulted in a large and temporally tight first transcriptional burst, followed by a refractory period in the range of hours. Our study thus reveals how different physiological stimuli can trigger kinetically distinct transcriptional responses of the same gene.
Carbon substitution for oxygen in silicates in planetary interiors

Significance Carbon is an important element in the Earth and other planets, but its concentration, chemical and structural form, and dynamics throughout the crust, mantle, and core are incompletely known. Based on the thermodynamic stability of a class of synthetic materials, the polymer-derived ceramics containing Si, C, and O, and on new NMR data for such systems containing a network-modifying metal (Li), this paper suggests that the substitution of C for O (rather than C for Si) in molten, amorphous, and crystalline silicate structures may provide a hitherto hidden reservoir of carbon in planetary interiors. Amorphous silicon oxycarbide polymer-derived ceramics (PDCs), synthesized from organometallic precursors, contain carbon- and silica-rich nanodomains, the latter with extensive substitution of carbon for oxygen, linking Si-centered SiOxC4-x tetrahedra. Calorimetric studies demonstrated these PDCs to be thermodynamically more stable than a mixture of SiO2, C, and silicon carbide. Here, we show by multinuclear NMR spectroscopy that substitution of C for O is also attained in PDCs with depolymerized silica-rich domains containing lithium, associated with SiOxC4-x tetrahedra with nonbridging oxygen. We suggest that significant (several percent) substitution of C for O could occur in more complex geological silicate melts/glasses in contact with graphite at moderate pressure and high temperature and may be thermodynamically far more accessible than C for Si substitution. Carbon incorporation will change the local structure and may affect physical properties, such as viscosity. Analogous carbon substitution at grain boundaries, at defect sites, or as equilibrium states in nominally acarbonaceous crystalline silicates, even if present at levels at 10–100 ppm, might form an extensive and hitherto hidden reservoir of carbon in the lower crust and mantle.
Prostaglandin E2 deficiency causes a phenotype of aspirin sensitivity that depends on platelets and cysteinyl leukotrienes

Significance Aspirin-exacerbated respiratory disease (AERD) is a common, severe variant of asthma, which is associated with overproduction of cysteinyl leukotrienes (cysLTs) and respiratory reactions to drugs that block cyclooxygenase 1. We demonstrate that mice selectively lacking the capacity to up-regulate the generation of prostaglandin E2 with inflammation develop an AERD-like phenotype that depends critically on platelets and thromboxane receptors, which drive transcellular synthesis of cysLTs, which, in turn, activate mast cells with aspirin challenge. The findings suggest a role for antiplatelet or thromboxane-selective antagonists as treatments for AERD. Aspirin-exacerbated respiratory disease (AERD) is characterized by asthma, tissue eosinophilia, overproduction of cysteinyl leukotrienes (cysLTs), and respiratory reactions to nonselective cyclooxygenase (COX) inhibitors. Ex vivo studies suggest that functional abnormalities of the COX-2/microsomal prostaglandin (PG)E2 synthase-1 system may underlie AERD. We demonstrate that microsomal PGE2 synthase-1 null mice develop a remarkably AERD-like phenotype in a model of eosinophilic pulmonary inflammation. Lysine aspirin (Lys-ASA)–challenged PGE2 synthase-1 null mice exhibit sustained increases in airway resistance, along with lung mast cell (MC) activation and cysLT overproduction. A stable PGE2 analog and a selective E prostanoid (EP)2 receptor agonist blocked the responses to Lys-ASA by ∼90%; EP3 and EP4 agonists were also active. The increases in airway resistance and MC products were blocked by antagonists of the type 1 cysLT receptor or 5-lipoxygenase, implying that bronchoconstriction and MC activation were both cysLT dependent. Lys-ASA–induced cysLT generation and MC activation depended on platelet-adherent granulocytes and T-prostanoid (TP) receptors. Thus, lesions that impair the inducible generation of PGE2 remove control of platelet/granulocyte interactions and TP-receptor–dependent cysLT production, permitting MC activation in response to COX-1 inhibition. The findings suggest applications of antiplatelet drugs or TP receptor antagonists for the treatment of AERD.
Patients’ experience of chronic lymphocytic leukaemia: baseline health‐related quality of life results from the LRF CLL4 trial

We examined the effects of active untreated chronic lymphocytic leukaemia (CLL) on health‐related quality of life (HRQoL), measured by the European Organization for Research and Treatment of Cancer quality of life questionnaire (EORTC QLQ‐C30) at randomisation into the Leukaemia Research Fund CLL4 trial. Patients were scored 0–100 within each of 15 domains. A difference between groups of ≥10 points was deemed clinically significant (asterisked * below). 431 valid baseline questionnaires were returned. Compared with population norms, patients had impaired HRQoL in 13/15 domains. The greatest differences were in fatigue*, sleep disturbance*, role functioning and global HRQoL. Fatigue was reported by 81% of patients, compared with the next most common symptoms: sleep disturbance (56%) and dyspnoea (49%). There was no association between spleen, liver or lymph node enlargement, or lymphocytosis and any HRQoL domain. Older age (≥70 years) was associated with poorer physical functioning (P < 0·001) but fewer financial difficulties (P < 0·001*). Impairment of HRQoL at baseline was most apparent in stage A‐progressive patients with B‐symptoms and stage C patients with haemoglobin <120 g/l: compared with all others, these patients had poorer physical, role and social functioning, more fatigue and dyspnoea and poorer global HRQoL (all P ≤ 0·001*). These findings support the recommendation to begin treatment when patients experience symptomatic disease, to improve HRQoL.
Iron indices and survival in maintenance hemodialysis patients with and without polycystic kidney disease.

BACKGROUND Anemia is less prominent in patients with polycystic kidney disease (PKD). Such iron indices as ferritin and transferrin saturation (TSAT) values are used to guide management of anemia in individuals on maintenance hemodialysis (MHD). Optimal levels of correction of anemia and optimal levels of TSAT and ferritin are unclear in chronic kidney disease patients and have not been studied specifically in PKD. METHODS We studied 2969 MHD patients with and 128 054 patients without PKD from 580 outpatient hemodialysis facilities between July 2001 and June 2006. Using baseline, time-dependent and time-averaged values with unadjusted and multivariable adjusted analysis models, the survival predictabilities of TSAT and ferritin were studied. RESULTS PKD patients were 58 ± 13 years old and included 46% women, whereas non-PKD patients were 62 ± 15 years old and 45% women. In both PKD and non-PKD patients, a time-averaged TSAT between 30 and 40% was associated with the lowest mortality. Time-averaged ferritin between 100 and <800 ng/mL was associated with the lowest mortality in PKD patients, although this range was 500 to <800 ng/mL in non-PKD patients. CONCLUSIONS In MHD patients with and without PKD, there was a U-shaped relationship between the average TSAT and mortality, and a TSAT of 30-40% was associated with the best survival. However, an average ferritin of 100-800 ng/mL was associated with the best survival in PKD patients, whereas that of non-PKD patients was 500-800 ng/mL. Further studies in PKD and non-PKD patients are necessary to determine whether or not therapeutic attempts to keep TSAT and ferritin levels in these ranges will improve survival.
The relative effect of manipulation and core rehabilitation in the treatment of acute mechanical lower back pain in athletes

Objectives The objectives were to compare the relative effect of manipulation and core rehabilitation in the treatment of acute mechanical lower back pain in athletes. Project Design: The study design was a randomized controlled parallel group trial. A quantitative study was performed, by making use of a pre Ã Ã Ã Â¢ and post experimental investigation (Nansel et al. 1993 and Naidoo, 2002). Setting: Participants presenting with acute low back pain with an onset of 7 days or less, to the Chiropractic Day Clinic at the Durban University of Technology. Subjects: Thirty athletic participants, either male or female, between the ages of 18 and 45 years presented at the initial consultation which included participant screening and establishment of their suitability for the study. These were then divided into either group A (which received a manipulation) or group B (which received core exercises). Outcome measure: A correct contraction of the core stability muscles was maintained, with a decrease in pressure (in mm Hg) on a Pressure Biofeedback Unit, and an increase in length of time (in seconds). Results: It was found that there was no significant difference between the manipulation and the core rehabilitation groups. Although both groups showed v improvement with regards to their acute mechanical low back pain, the core rehabilitation group improved at a significantly faster rate than the manipulation group with regards to endurance on the stabilizer. Conclusions: Both treatments were equally beneficial for most of the quantitative outcomes measured in this study. However, for the outcome of time on the stabilizer, the core rehabilitation group improved at a significantly faster rate than the manipulation group (p=0.006).
A comparative study of bone marrow and peripheral blood CD34+ myeloblasts in acute myeloid leukaemia

To examine the differences between primitive bone marrow (BM) and peripheral blood (PB) myeloblasts in acute myeloid leukaemia (AML), we compared CD34+ myeloblasts of paired BM and PB samples from 14 AML patients in terms of surface phenotype, homing and engraftment in a xenogeneic transplantation model, and gene expression, based on microarray studies and quantitative polymerase chain reaction. While there was no significant difference in surface phenotypes between these two populations, in vivo assay showed significantly better homing potential of PB CD34+ cells than BM CD34+ cells. Significant correlation between homing and engraftment in AML samples was also noted. In addition, gene expression profiling of CD34+ cells from five paired BM and PB leukaemic samples showed that genes involved in G‐protein and prostaglandin signalling, chemotaxis and stress response, cell proliferation and apoptosis were down‐regulated in PB CD34+ myeloblasts. These data suggested that circulating primitive myeloblasts in AML are functionally different from those residing in the marrow compartment, and such differences may be partly regulated by the BM microenvironment.
Keratins as the main component for the mechanical integrity of keratinocytes

Significance For decades, researchers have been trying to unravel one of the key questions in cell biology regarding keratin intermediate filament function in protecting epithelial cells against mechanical stress. For many different reasons, however, this fundamental hypothesis was still unproven. Here we answer this pivotal question by the use of keratin KO cells lacking complete keratin gene clusters to result in total loss of keratin filaments. This lack significantly softens cells, reduces cell viscosity, and elevates plastic cell deformation on force application. Reexpression of single keratin genes facilitates biomechanical complementation of complete cluster loss. Our manuscript therefore makes a very strong case for the crucial contribution of keratins to cell mechanics, with far-reaching implications for epithelial pathophysiology. Keratins are major components of the epithelial cytoskeleton and are believed to play a vital role for mechanical integrity at the cellular and tissue level. Keratinocytes as the main cell type of the epidermis express a differentiation-specific set of type I and type II keratins forming a stable network and are major contributors of keratinocyte mechanical properties. However, owing to compensatory keratin expression, the overall contribution of keratins to cell mechanics was difficult to examine in vivo on deletion of single keratin genes. To overcome this problem, we used keratinocytes lacking all keratins. The mechanical properties of these cells were analyzed by atomic force microscopy (AFM) and magnetic tweezers experiments. We found a strong and highly significant softening of keratin-deficient keratinocytes when analyzed by AFM on the cell body and above the nucleus. Magnetic tweezers experiments fully confirmed these results showing, in addition, high viscous contributions to magnetic bead displacement in keratin-lacking cells. Keratin loss neither affected actin or microtubule networks nor their overall protein concentration. Furthermore, depolymerization of actin preserves cell softening in the absence of keratin. On reexpression of the sole basal epidermal keratin pair K5/14, the keratin filament network was reestablished, and mechanical properties were restored almost to WT levels in both experimental setups. The data presented here demonstrate the importance of keratin filaments for mechanical resilience of keratinocytes and indicate that expression of a single keratin pair is sufficient for almost complete reconstitution of their mechanical properties.
The Stanford V regimen is effective in patients with good risk Hodgkin lymphoma but radiotherapy is a necessary component

One‐hundred and thirteen patients between the ages of 15 and 88 years with biopsy proven, untreated Hodgkin lymphoma were treated by physicians in the Nebraska Lymphoma Study Group using the Stanford V regimen (bleomycin, doxorubicin, etoposide, mechlorethamine, prednisone, vinblastine and vincristine) between January 1997 and January 2006. With a median follow‐up of all surviving patients of 63 months, the 5‐year overall survival (OS) was 84% and the 5‐year progression‐free survival (PFS) was 74%. Age >60 years, other than nodular sclerosing histological subtype, Ann Arbor Stage III/IV, and the presence of B‐symptoms significantly predicted treatment outcome. Patients with 0–2 of these factors had a 5‐year PFS and OS of 80% and 89% vs. 20% and 40% for patients with 3 or 4 factors. Patients who received radiotherapy had a superior 5‐year PFS (86% vs. 42%) and OS (96% vs. 53%). Patients with 0–2 adverse risk factors who received radiotherapy had an excellent treatment outcome with 5‐year PFS of 88% and a 5‐year OS of 97%. The Stanford V chemotherapy regimen has an excellent treatment outcome for good prognosis patients with Hodgkin lymphoma. The results are compromised when radiotherapy is not utilized.