Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization and Evolution of Cell Division and Cell Wall Synthesis Genes in the Bacterial Phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and Phylogenetic Comparison with rRNA Genes

ABSTRACT In the past, studies on the relationships of the bacterial phyla Planctomycetes, Chlamydiae, Lentisphaerae, and Verrucomicrobia using different phylogenetic markers have been controversial. Investigations based on 16S rRNA sequence analyses suggested a relationship of the four phyla, showing the branching order Planctomycetes, Chlamydiae, Verrucomicrobia/Lentisphaerae. Phylogenetic analyses of 23S rRNA genes in this study also support a monophyletic grouping and their branching order—this grouping is significant for understanding cell division, since the major bacterial cell division protein FtsZ is absent from members of two of the phyla Chlamydiae and Planctomycetes. In Verrucomicrobia, knowledge about cell division is mainly restricted to the recent report of ftsZ in the closely related genera Prosthecobacter and Verrucomicrobium. In this study, genes of the conserved division and cell wall (dcw) cluster (ddl, ftsQ, ftsA, and ftsZ) were characterized in all verrucomicrobial subdivisions (1 to 4) with cultivable representatives (1 to 4). Sequence analyses and transcriptional analyses in Verrucomicrobia and genome data analyses in Lentisphaerae suggested that cell division is based on FtsZ in all verrucomicrobial subdivisions and possibly also in the sister phylum Lentisphaerae. Comprehensive sequence analyses of available genome data for representatives of Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes strongly indicate that their last common ancestor possessed a conserved, ancestral type of dcw gene cluster and an FtsZ-based cell division mechanism. This implies that Planctomycetes and Chlamydiae may have shifted independently to a non-FtsZ-based cell division mechanism after their separate branchings from their last common ancestor with Verrucomicrobia.
Balancing risk versus benefit: the elderly patient’s perspective on warfarin therapy

Warfarin therapy is underused in the target at-risk elderly population. Clinicians perceive that older patients are reluctant to use this therapy, however the perspective of patients or their carers has yet to be explored. Objective: To explore in-depth the perspectives of elderly patients and/or their carers regarding the use of warfarin therapy. Method: A qualitative study, using semi-structured group interviews was undertaken. The audio-taped discussions were transcribed verbatim, then thematically analysed to identify emergent themes. Group discussions were conducted at a major Sydney teaching hospital, over a 2-month period. Individuals aged 65 years or older (and/or their carers) who were using long-term (6 months) warfarin therapy were recruited by voluntary response to study flyers. Results: 17 patients and carers (mean age 77.2 SD=7.5 years) participated in one of two focus groups. Five core themes emerged regarding warfarin therapy: inadequate knowledge and understanding about it, patients/carers variable experience of information provision, cycle of reactions to being on it, issues in its practical management, and the spectrum of experiences with it. Overall, participants were very accepting of the therapy, describing a high level of compliance, despite initial fears and anxieties, and a relative lack of knowledge. Patients felt somewhat abandoned in their management of warfarin due to the lack of ongoing support services in the community, and inadequate information provision. Conclusions: Elderly patients and their carers appear to be quite accepting of warfarin therapy, in contrast to the perceptions of health care professionals. More effort is needed, however, in terms of information provision, particularly in the form of community-based services, to assist patients in the long-term management of warfarin.
Antibody and Cytokine Responses to the Cilium-Associated Respiratory Bacillus in BALB/c and C57BL/6 Mice

ABSTRACT The cilium-associated respiratory (CAR) bacillus is a gram-negative, gliding bacterium that causes persistent respiratory tract infections in rodents despite histologic and serologic evidence of a marked immune response. To assess humoral immunity and cytokine responses in CAR bacillus disease, 6-week-old female BALB/c and C57BL/6 mice were inoculated intratracheally with 105 CAR bacillus organisms. CAR bacillus-specific serum immunoglobulins (immunoglobulin M [IgM], IgG1, IgG2a, IgG2b, IgG3, and IgA) and local pulmonary cytokines (tumor necrosis factor alpha [TNF-α], gamma interferon [IFN-γ], and interleukin-4 [IL-4]) were evaluated by enzyme-linked immunosorbent assay every 7 days for 49 days. BALB/c mice developed CAR bacillus-induced lesions early in the course of disease that became more severe with time. Correlating with increasing disease severity, BALB/c mice had elevations in all antibody isotypes tested, and elevations in pulmonary TNF-α, IFN-γ, and IL-4. C57BL/6 mice developed mild lesions with mild increases in serum IgM, IgG1, IgG2b, and IgG3 levels and minimally detectable IgG2a and IgA. Cytokine perturbations were not detected in C57BL/6 mice. The persistence of infection in BALB/c mice with vigorous serum antibody responses and increased IFN-γ and IL-4 responses suggests that humoral immunity and T-cell responses are ineffective at preventing CAR bacillus disease. Furthermore, the lackluster antibody responses and undetectable cytokine responses in C57BL/6 mice suggest that humoral immunity and T-cell responses are not critical in resistance to CAR bacillus-induced disease.
Cooperative Diversity for Virtual MIMO System in the Presence of Spatial Correlated Fading Model

In the existing papers on cooperative diversity, the fading channels are idealistically assumed to be Rayleigh fading channel. Taking into account the realistic propagation environments in the presence of spatial fading correlation, the performance of cooperative protocols using distributed space-time block code (DSTBC) in the two-ring scattering model is analyzed. The time division multiple access scheme is proposed with half duplex mode. Cooperative scheme is proposed, because cooperative diversity can combat the fading correlation by spatial decorrelation which is produced by independent multipaths and scattering paths between source nodes (SNs) and destination nodes (DNs). Cooperative relaying is shown to increase the link stability (or, alternatively, decrease the link outage probability) significantly. Therefore, the outage capacity and average bit error rate (BER) of cooperation are presented by applying various cooperative schemes in the correlated channel. Based on theoretical analyses and simulation results, the cooperative diversity yields significant performance gain in correlated channel, i.e., reducing the spatial correlation of each path and enhancing the overall performance of virtual MIMO system by high quality of cooperative interuser channel.
Low dose (0.05 units/kg/h) is comparable with standard dose (0.1 units/kg/h) intravenous insulin infusion for the initial treatment of diabetic ketoacidosis in children with type 1 diabetes—an observational study

Puttha R, Cooke D, Subbarayan A, Odeka E, Ariyawansa I, Bone M, Doughty I, Patel L, Amin R. Low dose (0.05 units/kg/h) is comparable with standard dose (0.1 units/kg/h) intravenous insulin infusion for the initial treatment of diabetic ketoacidosis in children with type 1 diabetes—an observational study
The histological structure of the malleolar groove of the fibula in man: its direct bearing on the displacement of peroneal tendons and their surgical repair

The peroneal (fibularis) tendons are held in place within the malleolar groove by the superior peroneal retinaculum. If this is torn, the tendons can subluxate or dislocate. Understanding the anatomy of the region is important for treating these injuries when it becomes necessary to reconstruct the malleolar groove surgically. Serial transverse sections of the groove were cut from 10 dissecting room cadavers after routine histology processing. The structure of the malleolar groove differed significantly in its proximal and distal parts. Distally, the bone is convex and the shape of the groove is determined by a thick periosteal cushion of fibrocartilage that covers the bone surface. Proximally, the groove shape is determined by the bone itself, and the periosteum is thin and fibrous. The restriction of a periosteal fibrocartilage to the distal end suggests that it serves to adapt the shape of the malleolar groove to that of the tendons within it and thus promotes stress dissipation. Paradoxically, however, it increases the risk of damage to subluxated tendons, because these can be sliced longitudinally by a sharp ridge created from periosteal fibrocartilage when the retinaculum is torn. Our results suggest that if bone‐block surgical procedures are used to reconstruct the malleolar groove, they are best restricted to its proximal part.
Gut Microbiota in Nymph and Adults of the Giant Mesquite Bug (Thasus neocalifornicus) (Heteroptera: Coreidae) Is Dominated by Burkholderia Acquired De Novo Every Generation

ABSTRACT The coreid bug Thasus neocalifornicus Brailovsky and Barrera, commonly known as the giant mesquite bug, is a ubiquitous insect of the southwestern United States. Both nymphs and adults are often found aggregated on mesquite trees (Prosopis spp.: Fabaceae) feeding on seedpods and plant sap. We characterized the indigenous bacterial populations of nymphs and adults of this species by using molecular and phylogenetic techniques and culturing methods. Results show that this insect's bacterial gut community has a limited diversity dominated by Burkholderia associates. Phylogenetic analysis by using 16s rRNA sequences suggests that these &bgr;-Proteobacteria are closely related to those symbionts obtained from other heteropteran midgut microbial communities but not to Burkholderia symbionts associated with other insect orders. These bacteria were absent from the eggs and were not found in all younger nymphs, suggesting that they are acquired after the insects have hatched. Rearing experiments of nymphs with potentially Burkholderia contaminated soil suggested that if this symbiont is not acquired, giant mesquite bugs experience higher mortality. Egg, whole-body DNA extractions of younger nymphs, and midgut DNA extractions of fifth-instar nymphs and adults also revealed the presence of &agr;-Proteobacteria from the Wolbachia genus. However, this bacterium was also present in reproductive organs of adults, indicating that this symbiont is not specific to the gut.
Influenza Viruses Select Ordered Lipid Domains during Budding from the Plasma Membrane*

During the budding of enveloped viruses from the plasma membrane, the lipids are not randomly incorporated into the envelope, but virions seem to have a lipid composition different from the host membrane. Here, we have analyzed lipid assemblies in three different viruses: fowl plague virus (FPV) from the influenza virus family, vesicular stomatitis virus (VSV), and Semliki Forest virus (SFV). Analysis of detergent extractability of proteins, cholesterol, phosphoglycerolipids, and sphingomyelin in virions showed that FPV contains high amounts of detergent-insoluble complexes, whereas such complexes are largely absent from VSV or SFV. Cholesterol depletion from the viral envelope by methyl-β-cyclodextrin results in increased solubility of sphingomyelin and of the glycoproteins in the FPV envelope. This biochemical behavior suggests that so-called raft-lipid domains are selectively incorporated into the influenza virus envelope. The “fluidity” of the FPV envelope, as measured by the fluorescence polarization of diphenylhexatriene, was significantly lower than compared with VSV or SFV. Furthermore, influenza virus hemagglutinin incorporated into the envelope of recombinant VSV was largely detergent-soluble, indicating the depletion of raft-lipid assemblies from this membrane. The results provide a model for lipid selectivity during virus budding and support the view of lipid rafts as cholesterol-dependent, ordered domains in biological membranes.
DNA Adenine Methylase Is Essential for Viability and Plays a Role in the Pathogenesis of Yersinia pseudotuberculosis andVibrio cholerae

ABSTRACT Salmonella strains that lack or overproduce DNA adenine methylase (Dam) elicit a protective immune response to differentSalmonella species. To generate vaccines against other bacterial pathogens, the dam genes of Yersinia pseudotuberculosis and Vibrio cholerae were disrupted but found to be essential for viability. Overproduction of Dam significantly attenuated the virulence of these two pathogens, leading to, in Yersinia, the ectopic secretion of virulence proteins (Yersinia outer proteins) and a fully protective immune response in vaccinated hosts. Dysregulation of Dam activity may provide a means for the development of vaccines against varied bacterial pathogens.
Circuit interpretation and perturbative analysis of differential-to-common mode conversion due to bend discontinuities

In this work, the mechanism of differential-to-common-mode (CM) conversion arising in differential interconnects due to bend discontinuities is investigated. A circuit interpretation of the phenomenon is provided in terms of lumped sources of interference included into the equivalent CM circuit. The obtained circuit model, assessed through full-wave simulation, allows inferring analogies and differences with respect to other sources of CM generation such as asymmetries and non-uniformities of the line cross-section, possibly occurring due to the manufacturing process. It is shown that the bent section can be interpreted as a local perturbation of an ideally uniform and symmetric microstrip cross-section and, as such, included into a more general simulation framework based on a perturbative approach aimed at the CM prediction in differential interconnects.
Limited V-shaped cement augmentation of the proximal femur to prevent secondary hip fractures

Patients with a femoral fracture due to osteoporosis are at high risk of sustaining a secondary fracture on the contralateral side. A prophylactic mechanical reinforcement of the contralateral side during operation of the initial fracture could be of interest for such patients. This biomechanical in vitro study investigates the potential of a limited V-shaped bone cement augmentation to prevent secondary hip fractures by targeting the areas of the proximal femur with the highest stresses during a fall. Five pairs of human cadaveric proximal femora were tested in a configuration simulating a fall on the greater trochanter. The femoral neck of one specimen of each pair was augmented with 8–14 ml polymethylmethacrylate from the lateral cortex towards inferior and superior, spanning a V-shaped cement pattern. Clinical relevant fractures were generated with a 45 kg mass in controlled free fall. Load-displacement data were recorded and energy to fracture, fracture load, yield load and stiffness were statistically evaluated. Augmented samples absorbed 124% more energy until fracture compared to their controls (p = 0.043). No significant differences were found between the two groups for fracture load (p = 0.5), yield load (p = 0.35) and stiffness (p = 0.5). Biomechanically, a limited V-shaped prophylactic cement augmentation carries potential to prevent secondary hip fractures indicated by increased energy absorption until fracture. Further investigations are necessary to minimize interference with the biology and to maximize the mechanical benefit of prophylactic augmentation.
Longitudinal trends in mental health among ethnic groups in Canada.

INTRODUCTION Immigration continues to transform the ethnic composition of the Canadian population. We investigated whether longitudinal trends in mental distress vary between seven cultural and ethnic groups and whether mental distress within the same ethnic group varies by demographic (immigrant status, sex, age, marital status, place and length of residence), socio-economic (education, income), social support and lifestyle factors. METHOD The study population consisted of 14 713 respondents 15 years and older from the first six cycles of the National Population Health Survey (NPHS); 20% reported themselves to be immigrant at Cycle 1, in 1994/1995. The logistic regression model was fitted by modifying a multivariate quasi-likelihood approach, and robust variance estimates were obtained by using balanced repeated replication techniques. RESULTS Based on the multivariable model and self-reported data, we observed that female respondents were more likely to report moderate/high mental distress than male respondents; younger respondents more than older respondents; single respondents more than those in a relationship; urban-dwellers more than rural-dwellers; less educated respondents more than more educated respondents; current and former smokers more than non-smokers; and those living in a smoking household more than those living in non-smoking households. The relationship between ethnicity and mental distress was modified by immigrant status, sex, social involvement score and education. Confirming other research, we found an inverted U-shaped relationship between length of stay and mental distress: those who had lived in Canada for less than 2 years were less likely to report moderate/high mental distress, while those who had lived in Canada for 2 to 20 years were significantly more likely to report moderate/high mental distress than those who had lived in Canada for more than 20 years. CONCLUSION There is a need to develop ethnicity-specific mental health programs targeting those with low education attainment and low social involvement. Policies and programs should also target women, the younger age group (15-24 years) and low-income adequacy groups.
A 10 mm3 Inductive Coupling Radio for Syringe-Implantable Smart Sensor Nodes

We present a near-field radio system for a millimeter-scale wireless smart sensor node that is implantable through a 14-gauge syringe needle. The proposed system integrates a radio system on chip and a magnetic antenna on a glass substrate within a total dimension of 1 × 1 × 10 mm3. We demonstrate energy-efficient active near-field wireless communication between the millimeter-scale sensor node and a base station device through an RF energy-absorbing tissue. The wireless transceiver, digital baseband controller, wakeup controller, on-chip baseband timer, sleep timer, and MBUS controller are all integrated on the SoC to form a millimeter-scale sensor node, together with a 1 × 8 mm2 magnetic antenna fabricated with a 1.5-μm-thickness gold on a 100 μm-thickness glass substrate. An asymmetric link is established pairing the sensor antenna with a codesigned 11 × 11 cm2 base station antenna to achieve a link distance of up to 50 cm for sensor transmission and 20 cm for sensor reception. The transmitter consumes a 43.5 μW average power at 2 kb/s, while the receiver power consumption is 36 μW with a -54 dBm sensitivity at 100 kb/s. When powered by a 1×2.2 mm2 thin-film battery (2 μAh, 4.1 V), the designed system has a two week expected lifetime without battery recharging when the system wakes up and transmits and receives 16 b data every 10 min.
Psychiatric hospital admissions, behavioral risk factors, and all-cause mortality: the Scottish health survey.

BACKGROUND Emerging research is beginning to uncover a high prevalence of modifiable risk factors in patients with severe mental illness. We examined whether the association between episodes of psychiatric illness that involved hospitalization and all-cause mortality is mediated by behavioral risk factors. METHODS Data were collected from a nationally representative sample of 19 898 men and women from the Scottish Health Surveys (1995, 1998, and 2003) that were linked to a patient-based database of hospital admissions and deaths up to September 2006. There were 597 participants with at least 1 hospital admission for a psychiatric episode. RESULTS During a mean follow-up of 8.5 years, participants with a history of a psychiatric episode had a higher risk of all-cause mortality (age- and sex-adjusted hazard ratio, 3.25; 95% confidence interval, 2.63-4.02). In addition, they were more likely to be heavy smokers (odds ratio, 4.69; 95% confidence interval, 3.79-5.82), have low physical activity levels (2.24; 1.75-2.87), come from a lower socioeconomic group (2.17; 1.72-2.72), and be separated or divorced from their partner (2.02; 1.63-2.52). In multivariate analyses, the association between history of a psychiatric episode and all-cause mortality was attenuated but remained statistically significant (hazard ratio, 2.02; 95% confidence interval, 1.62-2.52; P<.001) after adjustments for psychosocial factors, smoking, physical activity, body mass index, and current mental health. CONCLUSIONS Behavioral risk factors may partly mediate the association between psychiatric episodes and mortality. These data highlight the need for prevention and treatment strategies among individuals with a history of severe mental illness.
Induction and Inhibition of Ciprofloxacin Resistance-Conferring Mutations in Hypermutator Bacteria

ABSTRACT The emergence of drug-resistant bacteria poses a serious threat to human health. Bacteria often acquire resistance from a mutation of chromosomal genes during therapy. We have recently shown that the evolution of resistance to ciprofloxacin in vivo and in vitro requires the induction of a mutation that is mediated by the cleavage of the SOS repressor LexA and the associated derepression of three specialized DNA polymerases (polymerase II [Pol II], Pol IV, and Pol V). These results led us to suggest that it may be possible to design drugs to inhibit these proteins and that such drugs might be coadministered with antibiotics to prevent mutation and the evolution of resistance. For the approach to be feasible, there must not be any mechanisms through which bacteria can induce mutations and acquire antibiotic resistance that are independent of LexA and its repressed polymerases. Perhaps the most commonly cited mechanism to elevate bacterial mutation rates is the inactivation of methyl-directed mismatch repair (MMR). However, it is unclear whether this represents a LexA-independent mechanism or if the mutations that arise in MMR-deficient hypermutator strains are also dependent on LexA cleavage and polymerase derepression. In this work, we show that LexA cleavage and polymerase derepression are required for the evolution of clinically significant resistance in MMR-defective Escherichia coli. Thus, drugs that inhibit the proteins responsible for induced mutations are expected to efficiently prevent the evolution of resistance, even in MMR-deficient hypermutator strains.
Dirty-Block Tracking in a Direct-Mapped DRAM Cache with Self-Balancing Dispatch

Recently, processors have begun integrating 3D stacked DRAMs with the cores on the same package, and there have been several approaches to effectively utilizing the on-package DRAMs as caches. This article presents an approach that combines the previous approaches in a synergistic way by devising a module called the dirty-block tracker to maintain the dirtiness of each block in a dirty region. The approach avoids unnecessary tag checking for a write operation if the corresponding block in the cache is not dirty. Our simulation results show that the proposed technique achieves a 10.3% performance improvement on average over the state-of-the-art DRAM cache technique.