Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the requirements for pilus biogenesis at the outer membrane usher and the function of the usher C‐terminus

Uropathogenic strains of Escherichia coli assemble type 1 and P pili to colonize the bladder and kidney respectively. These pili are prototype structures assembled by the chaperone/usher secretion pathway. In this pathway, a periplasmic chaperone works together with an outer membrane (OM) usher to control the folding of pilus subunits, their assembly into a pilus fibre and secretion of the fibre to the cell surface. The usher serves as the assembly and secretion platform in the OM. The usher has distinct functional domains, with the N‐terminus providing the initial targeting site for chaperone–subunit complexes and the C‐terminus required for subsequent stages of pilus biogenesis. In this study, we investigated the molecular interactions occurring at the usher during pilus biogenesis and the function of the usher C‐terminus. We provide genetic and biochemical evidence that the usher functions as a complex in the OM and that interaction of the pilus adhesin with the usher is critical to prime the usher for pilus biogenesis. Analysis of C‐terminal truncation and substitution mutants of the P pilus usher PapC demonstrated that the C‐terminus is required for proper binding of chaperone–subunit complexes to the usher and plays an important role in assembly of complete pili.
Clostridium oceanicum, sp. n., a Sporeforming Anaerobe Isolated from Marine Sediments

Fourteen strains of a terminal-spored anaerobe were isolated from marine sediments obtained off the Atlantic and Pacific coasts of tropical South America. These strains are proteolytic, lecithinolytic, only slightly saccharolytic, often form cells with two spores, and appear unlike any described species of terminal-spored, proteolytic anaerobe. The name Clostridium oceanicum is suggested. The type strain (no. 25647) is deposited in the American Type Culture Collection.
Phylogeography and evolution of a fungal–insect association on the Tibetan Plateau

Parasitoidism refers to a major form of interspecies interactions where parasitoids sterilize and/or kill their hosts typically before hosts reach reproductive age. However, relatively little is known about the evolutionary dynamics of parasitoidism. Here, we investigate the spatial patterns of genetic variation of Chinese cordyceps, including both the parasitoidal fungus Ophiocordyceps sinensis and its host insects. We sampled broadly from alpine regions on the Tibetan Plateau and obtained sequences on seven fungal and three insect DNA fragments from each of the 125 samples. Seven and five divergent lineages/cryptic species were identified within the fungus and host insects, respectively. Our analyses suggested that O. sinensis and host insects originated at similar geographic regions in southern Tibet/Yunnan, followed by range expansion to their current distributions. Cophylogenetic analyses revealed a complex evolutionary relationship between O. sinensis and its host insects. Significant congruence was found between host and parasite phylogenies and the time estimates of divergence were similar, raising the possibility of the occurrence of cospeciation events, but the incongruences suggested that host shifts were also prevalent. Interestingly, one fungal genotype was broadly distributed, consistent with recent gene flow. In contrast, the high‐frequency insect genotypes showed limited geographic distributions. The dominant genotypes from both the fungus and the insect hosts may represent ideal materials from which to develop artificial cultivation of this important Chinese traditional medicine. Our results demonstrate that both historical and contemporary events have played important roles in the phylogeography and evolution of the O. sinensis–ghost moth parasitoidism on the Tibetan Plateau.
Bacterial and archaeal communities in the surface sediment from the northern slope of the South China Sea

Microbial diversity of sediments from the northern slope of the South China Sea was studied by constructing bacterial and archaeal 16S rRNA gene clone libraries. Fourteen bacterial phylogenetic groups were detected, including Gammaproteobacteria, Deltaproteobacteria, Planctomycetes, Alphaproteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Chloroflexi, Acidobacteria, Betaproteobacteria, Nitrospirae, candidate divisions OP8 and OP11, and an unknown group. Gammaproteobacteria was the predominant group in bacterial libraries with the percentage ranging from 31.8% to 63.2%. However, archaeal libraries had relatively lower diversity, with most clones belonging to marine archaeal group I uncultured Crenarchaeota. In addition, two novel euryarchaeal clones were detected not to match any culture-dependent or -independent isolates. Compared with other gas hydrate-rich ecosystems and different areas of the South China Sea, a distinct microbial community was revealed in this study.
Dynamics of epigenetic age following hematopoietic stem cell transplantation

With the awareness of an immunological graft- versus -leukemia (GvL) effect being able to eliminate residual leukemic cells, and, therefore, allowing the use of less intensive conditioning regimens, allogeneic hematopoietic stem cell transplantation (HSCT) is now widely used as a curative therapy
A novel biotin protein required for reductive carboxylation of 2‐oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK‐6

Isocitrate dehydrogenase was purified from Hydrogenobacter thermophilus, and the corresponding gene was cloned and sequenced. The enzyme had similar structural properties to the isocitrate dehydrogenase of Escherichia coli, but differed in its catalytic properties, such as coenzyme specificity, pH dependency and kinetic parameters. Notably, the enzyme catalysed the oxidative decarboxylation of isocitrate, but not the reductive carboxylation of 2‐oxoglutarate. The carboxylation reaction required the addition of cell extract and ATP‐Mg, suggesting the existence of additional carboxylation factor(s). Further analysis of the carboxylation factor(s) resulted in the purification of two polypeptides. N‐terminal amino acid sequencing revealed that the two polypeptides are homologues of pyruvate carboxylase with a biotinylated subunit, but do not catalyse pyruvate carboxylation. Pyruvate carboxylase was also purified, but was not active in stimulating isocitrate dehydrogenase. Isocitrate dehydrogenase, the novel biotin protein, ATP‐Mg and NADH were essential for the reductive carboxylation of 2‐oxoglutarate. These observations indicate that the novel biotin protein is an ATP‐dependent factor, which is involved in the reverse (carboxylating) reaction of isocitrate dehydrogenase.
Precoding Schemes for the MIMO-GBC

The use of M antennas at the base station and of transmitter channel state information can boost the downlink throughput by a factor M (multiplexing gain), even though the receivers have a single antenna and do not cooperate. In this semi-tutorial work, we discuss some low-complexity alternatives to achieve a downlink throughput very close to the optimal sum capacity. We review and compare these alternatives and we show that, in the simple setting of independently fading channels, relatively traditional forms of linear beamforming achieve the best tradeoff between performance and complexity. These results somehow call for a reconsideration of the emphasis that certain recently proposed precoding techniques have enjoyed both in scientific literature and in technology development
2D electronically beam steerable integrated lens antennas for mmWave applications

Design of 2D electronically beam steerable integrated lens antennas (ILA) operating in the 73 GHz - 94 GHz frequency band is presented. Quartz extended hemispherical lenses with the diameters of 15 mm and 25 mm and extension lengths optimized with full-wave simulations are applied. Steering capabilities are provided by 8 or 16 switched antenna element arrays mounted on the back plane surface of the lens. The arrays are fabricated using standard high frequency multilayer printed circuit board technology Rogers RO4003C. Single pole 4 through (SP4T) switches from TriQuint Semiconductors and single pole double though (SPDT) switches from Hittite Microwave Corporation are used to implement the switching network. Electromagnetic simulation results of the designed antennas at 77 GHz show that the ILA with the 15 mm diameter lens provides scanning capabilities in any direction within the solid angles θ <; 17° and θ <; 25° (where θ = 0° direction is determined by the lens axis) for 8 and 16 element arrays respectively with the directivity of no less than 16 dBi. The ILA with the 25 mm diameter lens provides scanning capabilities in any direction within the solid angles θ <; 10° and θ <; 16° for 8 and 16 element arrays respectively with the directivity of no less than 20 dBi. The designed 2D electronically steerable ILAs can be used in different millimeter wave WLAN/WPAN applications and 77 GHz automotive radars.
Changes in the Ventilation of the Oxygen Minimum Zone of the Tropical North Atlantic

Changes in the ventilation of the oxygen minimum zone (OMZ) of the tropical North Atlantic are studied using oceanographic data from 18 research cruises carried out between 28.5° and 23°W during 1999–2008 as well as historical data referring to the period 1972–85. In the core of the OMZ at about 400-m depth, a highly significant oxygen decrease of about 15 μmol kg−1 is found between the two periods. During the same time interval, the salinity at the oxygen minimum increased by about 0.1. Above the core of the OMZ, within the central water layer, oxygen decreased too, but salinity changed only slightly or even decreased. The scatter in the local oxygen–salinity relations decreased from the earlier to the later period suggesting a reduced filamentation due to mesoscale eddies and/or zonal jets acting on the background gradients. Here it is suggested that latitudinally alternating zonal jets with observed amplitudes of a few centimeters per second in the depth range of the OMZ contribute to the ventilation of the OMZ. A conceptual model of the ventilation of the OMZ is used to corroborate the hypothesis that changes in the strength of zonal jets affect mean oxygen levels in the OMZ. According to the model, a weakening of zonal jets, which is in general agreement with observed hydrographic evidences, is associated with a reduction of the mean oxygen levels that could significantly contribute to the observed deoxygenation of the North Atlantic OMZ.
Birth Weight, Stress, and the Metabolic Syndrome in Adult Life

Abstract: There is now widespread agreement that small size at birth is associated with an increased risk of the metabolic syndrome (glucose intolerance, high blood pressure, and dyslipidemia) and related pathologies, including cardiovascular disease in later life. Evidence is emerging that suggests that programming of hormonal systems in response to an adverse fetal environment may be one of the mechanisms underlying these long‐term consequences of growth restriction in early life. In particular, alterations in neuroendocrine responses to stress may be important. Recent research suggests that increased adrenocortical and sympathoadrenal responses are associated with small size at birth. Epidemiological studies show that such physiological alterations in these neuroendocrine systems may have potent effects on risk of cardiovascular disease through their influence on risk factors, such as plasma glucose and lipid concentrations and blood pressure.
Reliability adjustment: A necessity for trauma center ranking and benchmarking

BACKGROUND Currently, trauma center quality benchmarking is based on risk adjusted observed-expected (O/E) mortality ratios. However, failure to account for number of patients has been recently shown to produce unreliable mortality estimates, especially for low-volume centers. This study explores the effect of reliability adjustment (RA), a statistical technique developed to eliminate bias introduced by low volume on risk-adjusted trauma center benchmarking. METHODS Analysis of the National Trauma Data Bank 2010 was performed. Patients 16 years or older with blunt or penetrating trauma and an Injury Severity Score (ISS) of 9 or greater were included. Based on the statistically accepted standards of the Trauma Quality Improvement Program methodology, risk-adjusted mortality rates were generated for each center and used to rank them accordingly. Hierarchical logistic regression modeling was then performed to adjust these rates for reliability using an empiric Bayes approach. The impact of RA was examined by (1) recalculating interfacility variations in adjusted mortality rates and (2) comparing adjusted hospital mortality quintile rankings before and after RA. RESULTS A total of 557 facilities (with 278,558 patients) were included. RA significantly reduced the variation in risk-adjusted mortality rates between centers from 14-fold (0.7–9.8%) to only 2-fold (4.4–9.6%) after RA. This reduction in variation was most profound for smaller centers. A total of 68 “best” hospitals and 18 “worst” hospitals based on current risk adjustment methods were reclassified after performing RA. CONCLUSION “Reliability adjustment” dramatically reduces variations in risk-adjusted mortality arising from statistical noise, especially for lower volume centers. Moreover, the absence of RA had a profound impact on hospital performance assessment, suggesting that nearly one of every six hospitals in National Trauma Data Bank would have been inappropriately placed among the very best or very worst quintile of rankings. RA should be considered while benchmarking trauma centers based on mortality.
Models of case management in long term home health care. The evolution of for-profit geriatric care management.

Professional geriatric care management has the potential to provide an emotionally satisfying, lucrative career for the social worker or nurse who is self-educated or who has formal continuing professional education in assessment, care options, and care coordination. Yet GCM as an organized profession, or as a career choice for the individual, requires institutional supports to grow and flourish. The GCM profession requires recognition by the states (including certification and credentialing). A network must be developed so that young persons can receive a first professional degree, or at least a concentration within nursing or social work, in the legal and financial implications of elder care as well as the biology of aging and the techniques of hands-on physical care of the elderly. Structures must be created for continuing professional education of the GCM practitioner. The various Medicaid programs that offer home care to the elderly and disabled rely heavily on assessment and case management; so does the entire Medicare system. However, the federal statutes and regulations do not explicitly authorize GCM participation in care planning. More to the point, they do not clearly authorize reimbursement of GCMs as independent professionals or as Medicare/Medicaid service providers. As private long-term care insurance evolves, GCM services should be recognized as proper components of the planning process (and therefore as services that can be reimbursed by the policy). Once this is done, the challenge for GCM professionals is to retain their focus on the needs of the elder and family, rather than to perceive themselves as gatekeepers who function to cut the cost of services instead of optimizing their variety and quality. (ABSTRACT TRUNCATED AT 250 WORDS)
Thiamine and Zinc in Prevention or Therapy of Lead Intoxication

Thiamine, zinc or their combination given through gastric gavage were investigated for their ability to prevent or treat experimental lead toxicity in rats. Simultaneous dietary supplementation with thiamine plus zinc was found to be the most effective way of reducing the lead-induced inhibition of δ-aminolevulinic acid dehydratase activity in blood, urinary excretion of δ-aminolevulinic acid and accumulation of lead in blood, liver and kidney. Prevention was more effective than post-lead exposure treatment which may be due mainly to the decrease in the absorption of lead in the gastro-intestinal tract in the presence of thiamine and/or zinc.
Managing fractures of the distal radius in adults: Clinical and research implications from systematic reviews of existing trials

adults. We undertook 2 systematic reviews with the support of the Cochrane Musculoskeletal Injuries Group (CMSIG); one of the 50 Collaborative Review Groups covering various aspects of health care in the Cochrane Collaboration. The latter international, not-for-proe t organization aims to help people make well-informed decisions about healthcare by preparing, maintaining and promoting the accessibility of systematic reviews of the effects of healthcare interventions. Further information can be obtained from the Collaboration’s World Wide Web site: http://www.cochrane. org.
Biphasic modulation of intracellular Ca2+ concentration by interleukin‐1β in cortical synaptosomes: involvement of a pertussis toxin‐sensitive G‐protein and mitogen‐activated protein kinase

The modulation of intracellular Ca2+ concentration ([Ca2+]i) by the pro-inflammatory cytokine interleukin-1β (IL-1β) was assessed in synaptosomes loaded with the Ca2+-sensitive dye, Fura-2AM. IL-1β was found to exert a biphasic effect on the KCl-induced rise in [Ca2+]i, extending an inhibitory effect at lower (3.5 ng/ml) concentrations, and a stimulatory effect at high (100 ng/ml) concentrations. The inhibitory action of IL-1β on [Ca2+]i was sensitive to pertussis toxin (PTX; 2 μg/ml), indicating a role for a PTX-sensitive G-protein, but was unaffected by the p42 mitogen-activated protein kinase kinase (MAP kinase kinase) inhibitor, PD 098059 (2 μM). In contrast, the stimulatory action of higher concentrations of IL-1β on [Ca2+]i was blocked by PD 098059 and unaffected by PTX. We conclude that the biphasic actions of IL-1β on the KCl-induced rise in [Ca2+]i are mediated through activation of alternative second messenger pathways.
Weight Status and Physical Activity in Third Graders with Chronic Health Conditions

Purpose: To describe weight status and physical activity levels of children with chronic health conditions and factors associated with high body mass index. Methods: Descriptive statistics and regression analysis were performed on data from a sample of third graders with and without chronic health conditions. Results: Children with asthma, sensory and physical disabilities were at greater risk than peers for overweight status. Children with chronic health conditions watched more television than peers, and their parents reported poorer physical and mental health. Higher body mass index was associated with physical inactivity, Hispanic ethnicity and living in urban areas, more nonparental care arrangements, fewer siblings, low socioeconomic status, increased television viewing, asthma, and poor parental mental and physical health. Conclusions: Results support family-centered care for all children with chronic health conditions, and interventions to increase physical activity in children with asthma, sensory, and physical disabilities.
Laminar restriction of retinal macrophagic response to optic nerve axotomy in the rat.

Following optic nerve transection, most of the retinal ganglion cells die. Their debris is promptly cleared by phagocytic cells. It is currently not known to what extent peripherally derived macrophages contribute to this activity. Using antibodies OX42 and ED-1, phagocytic cells were labeled in the retinas of optic nerve lesioned adult rats. To distinguish whether the cells were reactive microglial or macrophagic in origin, blood-borne monocytes were labeled with fluorescent microspheres while in the systemic circulation. Macrophages invaded the retina, but only in the nerve fiber layer, sparing the ganglion cell and other layers. These macrophages engulfed only the axonal debris from dying ganglion cells, not their degenerating cell bodies. These results indicate that although peripherally derived monocytic cells are recruited into the retrogradely degenerating retina, their role in clearing debris is limited to the optic fiber layer.
The Expression of p18INK4 and p27kip1 Cyclin-Dependent Kinase Inhibitors Is Regulated Differently During Human B Cell Differentiation1

Cell cycle progression is under the control of cyclin-dependent kinases (cdks), the activity of which is dependent on the expression of specific cdk inhibitors. In this paper we report that the two cdk inhibitors, p27Kip1 and p18INK4c, are differently expressed and control different steps of human B lymphocyte activation. Resting B cells contain large amounts of p27Kip1 and no p18INK4c. In vitro stimulation by Staphylococcus aureus Cowan 1 strain or CD40 ligand associated with IL-10 and IL-2 induces a rapid decrease in p27Kip1 expression combined with cell cycle entry and progression. In contrast, in vitro Ig production correlates with specific expression of p18INK4c and early G1 arrest. This G1 arrest is associated with inhibition of cyclin D3/cdk6-mediated retinoblastoma protein phosphorylation by p18INK4c. A similar contrasting pattern of p18INK4c and p27Kip1 expression is observed both in B cells activated in vivo and in various leukemic cells. Expression of p18INK4c was also detected in various Ig-secreting cell lines in which both maximum Ig secretion and specific p18INK4c expression were observed during the G1 phase. Our study shows that p27Kip1 and p18INK4c have different roles in B cell activation; p27Kip1 is involved in the control of cell cycle entry, and p18INK4c is involved in the subsequent early G1 arrest necessary for terminal B lymphocyte differentiation.
Effects of several antifungal drug combinations against clinical and environmental isolates of Cryptococcus neoformans from China

The in vitro interactions of caspofungin (CSP) with terbinafine (TRB) and ravuconazole (RVC) with 5‐fluorocytosine (5‐FC) were tested against 82 clinical and environmental isolates of Cryptococcus neoformans from China. The interaction of CSP with TRB proved synergistic against those isolates with a CSP MIC ≤2 μg ml−1 (5% of the isolates), additive against 42% of the isolates and indifferent against 53%. The effects of RVC with 5‐FC were synergistic, additive or indifferent against 8%, 26% and 67% of the isolates, respectively. No antagonistic effects were found among any of the drugs. The combinations of CSP with TRB and RVC with 5‐FC may display beneficial effects in a strain‐dependent manner, while in no case showed antagonistic effects. These data might be of use to design safer and more efficient treatments for patients with cryptococcosis and warrant further evaluation.
Can Government Purchases Stimulate the Economy

This essay briefly reviews the state of knowledge about the government spending multiplier. Drawing on theoretical work, aggregate empirical estimates from the United States, as well as cross-locality estimates, I assess the likely range of multiplier values for the experiment most relevant to the stimulus package debate: a temporary, deficit-financed increase in government purchases. I conclude that the multiplier for this type of spending is probably between 0.8 and 1.5. ( JEL E23, E62, H50)