Miracle-dz/UniFAR-FTUs huggingface dataset:
Expansion of pneumococcal serotype 23F and 14 lineages with genotypic changes in capsule polysaccharide locus and virulence gene profiles post introduction of pneumococcal conjugate vaccine in Blantyre, Malawi

Since the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Malawi in 2011, there has been persistent carriage of vaccine serotype (VT) Streptococcus pneumoniae, despite high vaccine coverage. To determine if there has been a genetic change within the VT capsule polysaccharide (cps) loci since the vaccine’s introduction, we compared 1,022 whole-genome-sequenced VT isolates from 1998 to 2019. We identified the clonal expansion of a multidrug-resistant, penicillin non-susceptible serotype 23F GPSC14-ST2059 lineage, a serotype 14 GPSC9-ST782 lineage and a novel serotype 14 sequence type GPSC9-ST18728 lineage. Serotype 23F GPSC14-ST2059 had an I253T mutation within the capsule oligosaccharide repeat unit polymerase Wzy protein, which is predicted in silico to alter the protein pocket cavity. Moreover, serotype 23F GPSC14-ST2059 had SNPs in the DNA binding sites for the cps transcriptional repressors CspR and SpxR. Serotype 14 GPSC9-ST782 harbour a non-truncated version of the large repetitive protein (Lrp), containing a Cna protein B-type domain which is also present in proteins associated with infection and colonisation. These emergent lineages also harboured genes associated with antibiotic resistance, and the promotion of colonisation and infection which were absent in other lineages of the same serotype. Together these data suggest that in addition to serotype replacement, modifications of the capsule locus associated with changes in virulence factor expression and antibiotic resistance may promote vaccine escape. In summary, the study highlights that the persistence of vaccine serotype carriage despite high vaccine coverage in Malawi may be partly caused by expansion of VT lineages post PCV13 rollout. Impact Statement Our findings highlight the potential for clonal expansion of multidrug-resistant, penicillin-non-susceptible vaccine serotype lineages with capsule locus modifications, within a high carriage and disease burden population. This shift has occurred among young children where there has been high vaccine coverage, posing challenges for effective vaccine scheduling and design. Furthermore, this study emphasises the importance of ongoing Streptococcus pneumoniae genomic surveillance as new or modified pneumococcal vaccines are implemented. 2. Data summary Whole genome sequencing assemblies for the PCVPA survey have been deposited in the BioProject PRJNA1011974.
Full-length structure of the host targeted bacterial effector Bep1 reveals a novel structural domain conserved in FIC effector proteins from Bartonella

Bacterial effector proteins translocated via a type-IV secretion system (T4SS) typically harbor a C-terminal segment required for recognition by the type-IV secretion coupling protein 1. In the α-proteobacterial pathogen Bartonella, the signal is bipartite being composed of a BID (Bep intracellular delivery) domain and a positively charged C-terminal tail 2. Here, we show the crystal structure of full length Bartonella effector protein 1 (Bep1), which shows a novel FIC – OB – BAS(BID) domain arrangement conserved in the majority of Beps with the BID domain inserted into the newly discovered BAS parent domain. We propose that the BAS domain is necessary for the overall “boomerang”-like shape of Bep1 and that it plays a role during translocation through the T4SS.
Validity and reliability of an FFQ for use with adolescents in Ho Chi Minh City, Vietnam

Abstract Objective The present study evaluates the reliability and validity of an FFQ designed for use with adolescents in urban Vietnam. Design A cohort study was conducted between December 2003 and June 2004. The FFQ was administered three times over a 6-month period (FFQ 1–3) and nutrient intakes were compared to those obtained from four 24 h recalls collected over the same period (24 h recalls 1–4) using crude, energy-adjusted and de-attenuated correlation coefficients. The level of agreement between the two measurements was also evaluated with Bland–Altman analysis. The percentage of nutrient intakes classified within one quintile, as well as quadratic-weighted kappa statistics, were calculated. Setting Ho Chi Minh City, Vietnam. Subjects A total of 180 students were recruited in three junior high schools. Results Coefficients ranged from 0·22 for retinol to 0·78 for fibre for short-term reliability, and from 0·30 for retinol to 0·81 for zinc for long-term reliability. Coefficients for nutrient intakes between the mean of the three FFQ and mean of four 24 h recalls were mostly around 0·40, but higher for energy-adjusted nutrients. After allowing for within-person variation, the mean coefficient was 0·52 for macronutrients and 0·46 for micronutrients. There were a relatively high proportion of nutrient intakes classified within one quintile and a small number grossly misclassified. Kappa values shows ‘fair’ to ‘good’ agreement for all food/nutrient categories, while the Bland–Altman plots indicated that the FFQ is accurate in assessing nutrient intake at a group level. Conclusions This newly developed FFQ is a valid tool for measuring nutrient intake in adolescents in urban Vietnam.
Investigation of the Fasciola Cinereum, Absent in BTBR mice, and Comparison with the Hippocampal Area CA2

The arginine vasopressin 1b receptor (Avpr1b) plays an important role in social behaviors including social learning, memory, and aggression, and is known to be a specific marker for the cornu ammonis area 2 (CA2) regions of the hippocampus. The fasciola cinereum (FC) is an anatomical region in which Avpr1b expressing neurons are prominent, but the functional roles of the FC have yet to be investigated. Surprisingly, the FC is absent in the inbred BTBR T+tf/J (BTBR) mouse strain used to study core behavioral deficits of autism. Here, we characterized and compared transcriptomic expression profiles using single nucleus RNA sequencing and identified 7 different subpopulations and heterogeneity within the dorsal CA2 (dCA2) and FC. Mef2c, involved in autism spectrum disorder, is more highly expressed in the FC. Using Hiplex in situ hybridization, we examined the neuroanatomical locations of these subpopulations in the proximal and distal regions of the hippocampus. Anterograde tracing of Avpr1b neurons specific for the FC showed projections to the IG, dCA2, lacunosum molecular layer of CA1, dorsal fornix, septofibrial nuclei, and intermediate lateral septum (iLS). In contrast to the dCA2, inhibition of Avpr1b neurons in the FC by the inhibitory DREADD system during behavioral testing did not impair social memory. We performed single nucleus RNA sequencing in the dCA2 region and compared between wildtype (WT) and BTBR mice. We found that transcriptomic profiles of dCA2 neurons between BTBR and WT mice are very similar as they did not form any unique clusters; yet, we found there were differentially expressed genes between the dCA2s of BTBR and WT mice. Overall, this is a comprehensive study of the comparison of Avpr1b neuronal subpopulations between the FC and dCA2. The fact that FC is absent in BTBR mice, a mouse model for autism spectrum disorder, suggests that the FC may play a role in understanding neuropsychiatric disease.
Interleaved ZVS Converter With Ripple-Current Cancellation

In this paper, an interleaved soft-switching converter with ripple-current cancellation is presented to achieve zero- voltage-switching (ZVS) turn-on and load current sharing. In order to achieve ZVS turn-on, an active snubber is connected in parallel with the primary winding of the transformer. The energy stored in the transformer leakage inductance and magnetizing inductance can be recovered so that the peak voltage stress of switching devices is limited. The resonance at the transition interval is used to realize ZVS turn-on of all switches. In order to achieve three-level pulsewidth-modulation (PWM) scheme, an addition fast-recovery diode is used in the converter. Three-level PWM scheme can reduce the ac ripple current on the output inductor such that the output inductor can be reduced. The current-doubler rectifier is adopted in the secondary side of the transformer to reduce the transformer secondary-winding current and output voltage ripple by canceling the current ripple of two output inductors. The output voltage is controlled at the desired value using the interleaved PWM scheme. These features make the proposed converter suitable for the dc-dc converter with high output current. The operation principles, steady state analysis, and design equations of the proposed converter are provided in detail. Finally, experiments based on a 600-W (12 V/50 A) prototype are provided to verify the effectiveness and feasibility of the proposed converter.
Novel assay for endangered Hong Kong grouper (Epinephelus akaara) to assess eDNA shedding, decay, and population status

Overexploitation is a major threat to marine ecosystems, causing collapse of numerous fisheries since the 19th century. The Hong Kong Grouper (Epinephelus akaara) is a commercial fish species that suffered at least 50-80% population declines in the past 40 years throughout its distribution range. Yet there has been minimal research or specific management, resulting in insufficient data on abundance, reproduction and habitat utilization. Here we aim to develop a novel species-specific quantitative PCR (qPCR) assay to detect potential occurrence of E. akaara through non-invasive environmental water samples. We developed a qPCR assay amplifying 71 bps of the mitochondrial ND2 gene which offers high sensitivity and specificity. To quantify the E. akaara population with the emerging environmental DNA (eDNA) tool, however, species-specific shedding and decay rates are crucial. The decay rate of E. akaara was similar to that of reported values of other marine fish species. However, the shedding rate of E. akaara was found to be few orders of magnitude lower which may be related to the relatively low activity and energy use from solitary and sedentary behavior of groupers. This highlights the importance of empirically determining species or taxon-specific shedding and decay rates to inform accurate abundance estimates with modelling tools for eDNA concentrations. Only 6 out of 88 water samples (6.81%) collected across 4 sampling seasons and 11 sites around Hong Kong showed positive signals at a concentration below limit of detection of the assay, implying its rarity in Hong Kong nowadays. Overall, we demonstrate that eDNA with our qPCR assay is efficient and sensitive in detecting the target species and is a promising tool in documenting endangered species for species management and conservation.
Prevalence of alpha-1 antitrypsin deficiency and allele frequency in patients with COPD in Brazil

ABSTRACT Objective: To determine the prevalence of alpha 1-antitrypsin (AAT) deficiency (AATD), as well as allele frequency, in COPD patients in Brazil. Methods: This was a cross-sectional study involving 926 COPD patients 40 years of age or older, from five Brazilian states. All patients underwent determination of AAT levels in dried blood spot (DBS) samples by nephelometry. Those with DBS AAT levels ≤ 2.64 mg/dL underwent determination of serum AAT levels. Those with serum AAT levels of < 113 mg/dL underwent genotyping. In case of conflicting results, SERPINA1 gene sequencing was performed. Results: Of the 926 COPD patients studied, 85 had DBS AAT levels ≤ 2.64 mg/dL, and 24 (2.6% of the study sample) had serum AAT levels of < 113 mg/dL. Genotype distribution in this subset of 24 patients was as follows: PI*MS, in 3 (12.5%); PI*MZ, in 13 (54.2%); PI*SZ, in 1 (4.2%); PI*SS, in 1 (4.2%); and PI*ZZ, in 6 (25.0%). In the sample as a whole, the overall prevalence of AATD was 2.8% and the prevalence of the PI*ZZ genotype (severe AATD) was 0.8% Conclusions: The prevalence of AATD in COPD patients in Brazil is similar to that found in most countries and reinforces the recommendation that AAT levels be measured in all COPD patients.
Critical thresholds in sea lice epidemics: evidence, sensitivity and subcritical estimation

Host density thresholds are a fundamental component of the population dynamics of pathogens, but empirical evidence and estimates are lacking. We studied host density thresholds in the dynamics of ectoparasitic sea lice (Lepeophtheirus salmonis) on salmon farms. Empirical examples include a 1994 epidemic in Atlantic Canada and a 2001 epidemic in Pacific Canada. A mathematical model suggests dynamics of lice are governed by a stable endemic equilibrium until the critical host density threshold drops owing to environmental change, or is exceeded by stocking, causing epidemics that require rapid harvest or treatment. Sensitivity analysis of the critical threshold suggests variation in dependence on biotic parameters and high sensitivity to temperature and salinity. We provide a method for estimating the critical threshold from parasite abundances at subcritical host densities and estimate the critical threshold and transmission coefficient for the two epidemics. Host density thresholds may be a fundamental component of disease dynamics in coastal seas where salmon farming occurs.
The FindMe Approach to Assisted Browsing

While the explosion of online information has introduced new opportunities for finding and using electronic data, it has also underscored the problem of isolating useful information and making sense of large, multidimensional information spaces. In response to this problem, we have developed an approach to building data tour guides, called FindMe systems. These programs know enough about an information space to help users navigate through it, making sure they not only come away with useful information but also insights into the structure of the information space itself. In these systems, we have combined the idea of instance-based browsing, which involves structuring retrieval around the critiquing of previously retrieved examples, and retrieval strategies, or knowledge-based heuristics for finding relevant information. This article illustrates these techniques with examples of working FindMe systems, and describes the similarities and differences between them. FindMe tour guides help users to select the perfect car, movie, restaurant, stereo or apartment on the World Wide Web.
Robust Hand Motion Tracking through Data Fusion of 5DT Data Glove and Nimble VR Kinect Camera Measurements

Vision based interfaces for human computer interaction have gained increasing attention over the past decade. This study presents a data fusion approach of the Nimble VR vision based system, using the Kinect camera, with the contact based 5DT Data Glove. Data fusion was achieved through a Kalman filter. The Nimble VR and filter output were compared using measurements performed on (1) a wooden hand model placed in various static postures and orientations; and (2) three differently sized human hands during active finger flexions. Precision and accuracy of joint angle estimates as a function of hand posture and orientation were determined. Moreover, in light of possible self-occlusions of the fingers in the Kinect camera images, data completeness was assessed. Results showed that the integration of the Data Glove through the Kalman filter provided for the proximal interphalangeal (PIP) joints of the fingers a substantial improvement of 79% in precision, from 2.2 deg to 0.9 deg. Moreover, a moderate improvement of 31% in accuracy (being the mean angular deviation from the true joint angle) was established, from 24 deg to 17 deg. The metacarpophalangeal (MCP) joint was relatively unaffected by the Kalman filter. Moreover, the Data Glove increased data completeness, thus providing a substantial advantage over the sole use of the Nimble VR system.
Exploratory Visual Analysis of Statistical Results from Microarray Experiments Comparing High and Low Grade Glioma

The biological interpretation of gene expression microarray results is a daunting challenge. For complex diseases such as cancer, wherein the body of published research is extensive, the incorporation of expert knowledge provides a useful analytical framework. We have previously developed the Exploratory Visual Analysis (EVA) software for exploring data analysis results in the context of annotation information about each gene, as well as biologically relevant groups of genes. We present EVA as a flexible combination of statistics and biological annotation that provides a straightforward visual interface for the interpretation of microarray analyses of gene expression in the most commonly occuring class of brain tumors, glioma. We demonstrate the utility of EVA for the biological interpretation of statistical results by analyzing publicly available gene expression profiles of two important glial tumors. The results of a statistical comparison between 21 malignant, high-grade glioblastoma multiforme (GBM) tumors and 19 indolent, low-grade pilocytic astrocytomas were analyzed using EVA. By using EVA to examine the results of a relatively simple statistical analysis, we were able to identify tumor class-specific gene expression patterns having both statistical and biological significance. Our interactive analysis highlighted the potential importance of genes involved in cell cycle progression, proliferation, signaling, adhesion, migration, motility, and structure, as well as candidate gene loci on a region of Chromosome 7 that has been implicated in glioma. Because EVA does not require statistical or computational expertise and has the flexibility to accommodate any type of statistical analysis, we anticipate EVA will prove a useful addition to the repertoire of computational methods used for microarray data analysis. EVA is available at no charge to academic users and can be found at http://www.epistasis. org.
Norms and Validity of the DriVR: A Virtual Reality Driving Assessment for Persons with Head Injuries

This article presents the results of two studies of a new driving simulator called "DriVR. " The first, normative study examined the performance of an uninjured driving population on the simulator. The driving ability of 148 participants in eight age categories was assessed using DriVR. The second, discriminative validity study examined DriVR's ability to discriminate between the performance of head-injured and uninjured adults. We administered the DriVR assessment to 17 head-injured adults. The performance of this group was compared to that of a subgroup of uninjured participants that matched the brain-injured participants in age, gender, and years of education. In general, DriVR's measures showed age-related changes in participant performance and were able to discriminate between head-injured and uninjured participants. These results suggested that age norms would be useful for analyzing the performance of head-injured clients who are being assessed with DriVR. It should be noted, however, that these studies did not examine DriVR's ability to predict performance in real, on-the-road tests.
Distance based duplex mode selection in large scale peer-to-peer wireless networks

A throughput analysis is conducted for a large scale peer-to-peer wireless network whose devices are capable of operating in both full- and half-duplex modes, using the tools of stochastic geometry. Each device selects its operating duplex mode based on the distance to its partner node. In both duplex modes, the energy consumption and the hardware configurations of the nodes are made equivalent for fair comparisons between full-duplex and half-duplex operations. Using the results of the analysis, an approach is proposed to determine a distance threshold value for duplex mode selection, and the proposed distance threshold can be computed offline. It is found that the throughput performance of the hybrid full-/half-duplex network generated with the proposed distance threshold based duplex mode selection technique outperforms both the pure half-duplex and pure full-duplex network settings for most practically common network parameter values.
Processed Meat and Colorectal Cancer Risk: A Pooled Analysis of Three Italian Case-Control Studies

ABSTRACT To add evidence to the limited data available from southern Europe, we assessed the association between processed meat consumption and colorectal cancer risk. We analyzed data from three case-control studies conducted between 1985 and 2010 in various Italian areas, including a total of 3745 incident cases and 6804 hospital-based controls. We calculated odds ratios (ORs) and 95% confidence intervals (CIs) by unconditional multiple logistic regression models. The median consumption of processed meat was around 20 g/day both in cases and controls. The OR of colorectal cancer was 1.02 (95% CI 0.99–1.04) for an increase of 10 g/day of processed meat. The association was statistically significant for colon cancer (OR 1.03, 95% CI 1.00–1.06), particularly for proximal colon cancer (OR 1.09, 95% CI 1.04–1.14), while there was no relation with rectal cancer (OR 0.99, 95% CI 0.95–1.03). The OR of proximal colon cancer was 1.38 (95% CI 1.08–1.75) for the highest sex-specific tertile of consumption (>25 g/day for men, >21.5 for women) compared with the lowest (<15 g/day), whereas no significant ORs were found for other anatomical subsites. Our findings indicate that there is no association with colorectal cancer overall, in the presence, however, of a positive association with proximal colon cancer.
REINFORCE: Achieving Efficient Failure Resiliency for Network Function Virtualization-Based Services

Ensuring high availability (HA) for software-based networks is a critical design feature that will help the adoption of software-based network functions (NFs) in production networks. It is important for NFs to avoid outages and maintain mission-critical operations. However, HA support for NFs on the critical data path can result in unacceptable performance degradation. We present REINFORCE, an integrated framework to support efficient resiliency for NF service chains. REINFORCE includes timely failure detection and consistent failover mechanisms. REINFORCE replicates state to standby NFs (local and remote) while enforcing correctness. It minimizes the number of state transfers by exploiting the concept of external synchrony, and leverages opportunistic batching and multi-buffering to optimize performance. Experimental results show that, even at line-rate packet processing (10 Gbps), REINFORCE achieves chain-level failover across servers in a LAN within 10ms, incurring less than 10% performance overhead, and adds average latency only <inline-formula> <tex-math notation="LaTeX">$\sim 400~\mu \text{s}$ </tex-math></inline-formula>, with a worst-case latency of less than 1ms. REINFORCE also recovers from software failures within the same node in less than <inline-formula> <tex-math notation="LaTeX">$100~\mu \text{s}$ </tex-math></inline-formula>, incurring less than 1% performance overhead and adds less than <inline-formula> <tex-math notation="LaTeX">$5~\mu \text{s}$ </tex-math></inline-formula> latency during normal operation.