Miracle-dz/UniFAR-FTUs huggingface dataset:
Racial Disparities Associated with the Prevalence of Vaccine and Non-Vaccine HPV Types and Multiple HPV Infections between Asia and Africa: A Systematic Review and Meta-Analysis

Background/Objective: Cervical Cancer is the 6th most common and 3rd most deadly cancer among women. Despite the fact that the majority of the countries in Asia and Africa have a similar economy and low life expectancy, the mean age-standardized incidence rate (ASIR) of cervical cancer is substantially higher in Africa than in Asia. This study identified the correlates of the higher ASIR rates in Africa relative to Asia against two timelines; 2004-2009 and 2010-2017. Methods: Peer-reviewed articles published between 2004 and 2017 were selected using the PRISMA standard. Sources of articles included Google Scholar, Scopus, PubMed Central, and EMBASE. Search keywords included: HPV genotypes, cervical cancer, HPV vaccine, and multiple infections in Africa and Asia. Result: Twenty-nine and seventeen full-length articles were selected from Africa and Asia, respectively. The pooled prevalence of HPV infection up to 2017 was higher in Africa (41.8%; 95% CI: 35.9, 47.7) than in Asia (24.2%; 95% CI: 16.22, 32.2) at p< 0.001. Between 2004-2009 and 2010-2017 timelines, the pooled prevalence of HPV infection decreased from 49.1% to 36.7% (OR’: 1.66, 95% CI: 1.51-1.80) in Africa and increased from 16.9% to 20.5% (OR’: 0.79, 95% CI: 0.71-0.86) in Asia. However, the pooled prevalence of multiple HPV infections and non-vaccine high-risk HPV infections were higher among African women diagnosed with cancer (30.9% and 5.2%) than their Asian counterparts (21.0% and 2.0%, respectively) at p< 0.001. Additionally, the pooled prevalence of the five most prevalent high-risk HPV types in Africa were HPV16 (35.3%), HPV52 (14.2%), HPV35 (12.4%), HPV18 (10.4%), and HPV58 (10.0%), while that of Asia were HPV16 (37.3%), HPV52 (16.2%), HPV58 (14.7%), HPV33 (7.4%) and HPV18 (7.2%). Conclusion: This study suggests that the higher prevalence of HPV, multiple HPV and non-vaccine HPV infections could be responsible for the higher ASIR in Africa than in Asia.
Non‐invasive estimation of the depth profile of soil strength with acoustic‐to‐seismic coupling measurement in the presence of crops

A traditional penetrometer measurement of soil strength in terms of penetration resistance, a useful indicator of a soil's mechanical property, is invasive and manually laborious. An alternative non‐invasive technique uses an acoustic source, two microphones and a laser Doppler vibrometer to obtain acoustic‐to‐seismic (A–S) transfer functions. Transfer functions between the acoustically‐induced soil vibration and the acoustic signals have been compared, through numerical optimizations, with predictions of a wave‐propagation model for layered poro‐elastic media. The numerically optimized shear modulus of soil was converted to the soil strength equivalent of penetration resistance by applying an empirical relation for the type of soil in question. The A–S and penetrometer measurements were made in experimental fields planted with winter wheat. The depth profiles of A–S‐deduced soil strength agree reasonably with those of penetrometer readings in shallow layers of five arable plots. We have demonstrated that the strength of soil in the presence of growing crops can be measured by this non‐invasive approach.
Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA preprocessing chimeric reads.

The human gut bacteriophage community (phageome) plays an important role in the host's health and disease; however, the entire structure is poorly understood, partly owing to the generation of many incomplete genomes in conventional short-read metagenomics. Here, we show long-read metagenomics of amplified DNA of low-biomass phageomes with multiple displacement amplification (MDA), involving the development of a novel bioinformatics tool, SACRA, that efficiently preprocessed numerous chimeric reads generated through MDA. Using five samples, SACRA markedly reduced the average chimera ratio from 72% to 1.5% in PacBio reads with an average length of 1.8-kb. De novo assembly of chimera-less PacBio long reads reconstructed contigs of ≥ 5-kb with an average proportion of 27%, which was 1% in contigs from MiSeq short reads, thereby dramatically improving contig length and genome completeness. Comparison of PacBio and MiSeq contigs found MiSeq contig fragmentations frequently near local repeats and hypervariable regions in the phage genomes, and those caused by multiple homologous phage genomes coexisting in the community. We also developed a reference-independent method to assess the completeness of the linear phage genomes. Overall, we established a SACRA-coupled long-read metagenomics robust to highly diverse gut phageomes, identifying high-quality circular and linear phage genomes with adequate sequence quantity.
Topic modelling online depression forums: beyond narratives of self-objectification and self-blaming

Abstract Background Depression raises a double challenge: besides the negative mood and the intrusive thoughts, the relation to the self also becomes difficult. Online forums are analysed as communicative platforms enabling the interactive reconstruction of the self. Aims The discourses of online depression forums are explored. Firstly, narrative patterns are identified according to their thematic focus (e.g. dysfunctional body, challenges of intimacy) and discursive logic (e.g. information exchange, support). Secondly, narratives are analysed in order to describe various ways of grounding a depressed self. Methods ∼70.000 depression-related posts from the biggest English-speaking online forums (e.g. www.reddit.com/r/depression, www.healthunlocked.com) were analysed. Quantitative (LDA topic modelling) and qualitative (deep reading) approaches were used simultaneously to determine the optimal number of topics and their interpretation. Results 13 topics were identified and interpreted according to their content and communicative function. Based on the inter-topic distances four clusters were identified (medicalized, intimacy-oriented, critical and uninhabitable self-narratives). Conclusions The clusters of the 13 topics highlight various ways of narrating depression and the depressed self. Based on a comparison with a systematic review of mental illness recovery narratives, depression forums cover most narrative genres and emotional tones, thus create a unique opportunity for integrating the depressing experiences in the self.
Nonrandom Selection and Multiple Blood Feeding of Human Hosts by Anopheles Vectors: Implications for Malaria Transmission in Papua New Guinea

ABSTRACT. Nonrandom selection and multiple blood feeding of human hosts by Anopheles mosquitoes may exacerbate malaria transmission. Both patterns of blood feeding and their relationship to malaria epidemiology were investigated in Anopheles vectors in Papua New Guinea (PNG). Blood samples from humans and mosquito blood meals were collected in villages and human genetic profiles (“fingerprints”) were analyzed by genotyping 23 microsatellites and a sex-specific marker. Frequency of blood meals acquired from different humans, identified by unique genetic profiles, was fitted to Poisson and negative binomial distributions to test for nonrandom patterns of host selection. Blood meals with more than one genetic profiles were classified as mosquitoes that fed on multiple humans. The age of a person bitten by a mosquito was determined by matching the blood-meal genetic profile to the villagers’ genetic profiles. Malaria infection in humans was determined by PCR test of blood samples. The results show nonrandom distribution of blood feeding among humans, with biased selection toward males and individuals aged 15–30 years. Prevalence of Plasmodium falciparum infection was higher in this age group, suggesting males in this age range could be super-spreaders of malaria parasites. The proportion of mosquitoes that fed on multiple humans ranged from 6% to 13% among villages. The patterns of host utilization observed here can amplify transmission and contribute to the persistence of malaria in PNG despite efforts to suppress it with insecticidal bed nets. Excessive feeding on males aged 15–30 years underscores the importance of targeted interventions focusing on this demographic group.
Accuracy of the Veterans Health Administration COVID-19 (VACO) Index for predicting short-term mortality among 1307 US academic medical centre inpatients and 427 224 US Medicare patients

Background The Veterans Health Administration COVID-19 (VACO) Index predicts 30-day all-cause mortality in patients with COVID-19 using age, sex and pre-existing comorbidity diagnoses. The VACO Index was initially developed and validated in a nationwide cohort of US veterans—we now assess its accuracy in an academic medical centre and a nationwide US Medicare cohort. Methods With measures and weights previously derived and validated in US national Veterans Health Administration (VA) inpatients and outpatients (n=13 323), we evaluated the accuracy of the VACO Index for estimating 30-day all-cause mortality using area under the receiver operating characteristic curve (AUC) and calibration plots of predicted versus observed mortality in inpatients at a single US academic medical centre (n=1307) and in Medicare inpatients and outpatients aged 65+ (n=427 224). Results 30-day mortality varied by data source: VA 8.5%, academic medical centre 17.5%, Medicare 16.0%. The VACO Index demonstrated similar discrimination in VA (AUC=0.82) and academic medical centre inpatient population (AUC=0.80), and when restricted to patients aged 65+ in VA (AUC=0.69) and Medicare inpatient and outpatient data (AUC=0.67). The Index modestly overestimated risk in VA and Medicare data and underestimated risk in Yale New Haven Hospital data. Conclusions The VACO Index estimates risk of short-term mortality across a wide variety of patients with COVID-19 using data available prior to or at the time of diagnosis. The VACO Index could help inform primary and booster vaccination prioritisation, and indicate who among outpatients testing positive for SARS-CoV-2 should receive greater clinical attention or scarce treatments.
Pigment concentrations in eggshell and their related gene expressions in uterus of Changshun blue eggshell chickens

ABSTRACT 1. The goal of this study was to investigate the colour diversity of egg shells and expression of related genes in the uterus of chickens that produce eggs of different colours. 2. Four colour types of Changshun blue-shell chickens, producing dark or light blue, greenish-brown and brown shelled eggs, were selected. The eggshell pigment concentration and colour values in each group were examined. The relative gene expression of solute carrier organic anion transporter family member 1C1 (SLCO1C1), ferrochelatase (FECH), haem oxygenase 1 (HO-1), ovotransferrin (OF) and biliverdin reductase A (BLVRA) in eggshell gland were measured. 3. The Δb, ΔE and protoporphyrin in brown and greenish-brown groups were significantly higher in the blue egg group (P < 0.01), whereas ΔL was significantly lower than that in the blue eggs (P < 0.01). There was no significant difference in biliverdin concentration between the brown and blue groups. 4. The Δa values, in descending order, were 8.27 ± 2.76 in the brown, −3.79 ± 2.39 in the greenish-brown and −7.29 ± 2.27 in the blue groups, respectively. The relative expression of HO-1 in the greenish-brown and light blue groups was significantly higher than in the dark blue and brown groups. The relative expression of FECH in the light blue group was significantly lower than that in the dark blue, greenish-brown or brown group (P < 0.01). The relative expression of HO-1 and BLVRA genes in the dark blue group was significantly higher than that in the light blue, greenish-brown and the brown group (P < 0.01). 5. The Δa might provide a better index than protoporphyrin and biliverdin contents for eggshell colour breeding. Overall, HO-1 as well as BLVRA were important candidate genes for the selection of dark blue eggs.
Competitive binding of MatP and topoisomerase IV to the MukB hinge domain

Structural Maintenance of Chromosomes (SMC) complexes have ubiquitous roles in compacting DNA linearly, thereby promoting chromosome organization-segregation. Interaction between the Escherichia coli SMC complex, MukBEF, and matS-bound MatP in the chromosome replication termination region, ter, results in depletion of MukBEF from ter, a process essential for efficient daughter chromosome individualization and for preferential association of MukBEF with the replication origin region. Chromosome-associated MukBEF complexes also interact with topoisomerase IV (ParC2E2), so that their chromosome distribution mirrors that of MukBEF. We demonstrate that MatP and ParC have an overlapping binding interface on the MukB hinge, leading to their mutually exclusive binding, which occurs with the same dimer to dimer stoichiometry. Furthermore, we show that matS DNA competes with the MukB hinge for MatP binding. Cells expressing MukBEF complexes that are mutated at the ParC/MatP binding interface are impaired in ParC binding and have a mild defect in MukBEF function. These data highlight competitive binding as a means of globally regulating MukBEF-topoisomerase IV activity in space and time.
Soil microbial sensitivity to temperature remains unchanged despite community compositional shifts along geothermal gradients

Climate warming may be exacerbated if rising temperatures stimulate losses of soil carbon to the atmosphere. The direction and magnitude of this carbon‐climate feedback are uncertain, largely due to lack of knowledge of the thermal adaptation of the physiology and composition of soil microbial communities. Here, we applied the macromolecular rate theory (MMRT) to describe the temperature response of the microbial decomposition of soil organic matter (SOM) in a natural long‐term warming experiment in a geothermally active area in New Zealand. Our objective was to test whether microbial communities adapt to long‐term warming with a shift in their composition and their temperature response that are consistent with evolutionary theory of trade‐offs between enzyme structure and function. We characterized the microbial community composition (using metabarcoding) and the temperature response of microbial decomposition of SOM (using MMRT) of soils sampled along transects of increasing distance from a geothermally active zone comprising two biomes (a shrubland and a grassland) and sampled at two depths (0–50 and 50–100 mm), such that ambient soil temperature and soil carbon concentration varied widely and independently. We found that the different environments were hosting microbial communities with distinct compositions, with thermophile and thermotolerant genera increasing in relative abundance with increasing ambient temperature. However, the ambient temperature had no detectable influence on the MMRT parameters or the relative temperature sensitivity of decomposition (Q10). MMRT parameters were, however, strongly correlated with soil carbon concentration and carbon:nitrogen ratio. Our findings suggest that, while long‐term warming selects for warm‐adapted taxa, substrate quality and quantity exert a stronger influence than temperature in selecting for distinct thermal traits. The results have major implications for our understanding of the role of soil microbial processes in the long‐term effects of climate warming on soil carbon dynamics and will help increase confidence in carbon‐climate feedback projections.
The best regimens for chemo-naïve incurable non-squamous non-small cell lung cancer with a programmed death-ligand 1, tumor proportion score 1–49%: a network meta-analysis

Background Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide. There is a rank order of the efficacy and safety of treatment options, including immune checkpoint inhibitors (ICIs), bevacizumab (Bev), and cytotoxic drugs. When patients have low programmed death-ligand 1 (PD-L1) expression, there are multiple options for treatment. In this study, we focused on ICI regimens in patients with non-squamous NSCLC with low PD-L1 expression and no driver alterations and assessed the efficacy of the regimens using network meta-analysis. Methods Randomized trials for incurable chemo-naïve non-squamous NSCLC were collected through electronic searches. The data were independently extracted and cross-checked by two investigators. The primary outcome of this analysis was overall survival (OS). A frequentist weighted least-squares approach random-model network meta-analysis was applied. Results Sixty-eight eligible studies and 22,619 patients were identified. Using a platinum + third-generation cytotoxic agent regimen (platinum regimen) as a reference, the platinum regimen + pembrolizumab (Pemb) [hazard ratio (HR) =0.55, 95% confidence interval (CI): 0.34–0.89, P=0.015] showed the best OS, followed by the platinum regimen + nivolumab (Niv) + ipilimumab (Ipi) (HR =0.61, 95% CI: 0.44–0.84, P=0.003) with no heterogeneity (I2=0%, P=0.348). Conclusions The addition of Pemb or Niv/Ipi to platinum-based chemotherapy seems to be a good therapeutic option for non-squamous NSCLC with a PD-L1 tumor proportion score (TPS) of 1–49%.
Loss of mTORC2‐induced metabolic reprogramming in monocytes uncouples migration and maturation from production of proinflammatory mediators

Monocyte migration to the sites of inflammation and maturation into macrophages are key steps for their immune effector function. Here, we show that mechanistic target of rapamycin complex 2 (mTORC2)‐dependent Akt activation is instrumental for metabolic reprogramming at the early stages of macrophage‐mediated immunity. Despite an increased production of proinflammatory mediators, monocytes lacking expression of the mTORC2 component Rictor fail to efficiently migrate to inflammatory sites and fully mature into macrophages, resulting in reduced inflammatory responses in vivo. The mTORC2‐dependent phosphorylation of Akt is instrumental for the enhancement of glycolysis and mitochondrial respiration, required to sustain monocyte maturation and motility. These observations are discussed in the context of therapeutic strategies aimed at selective inhibition of mTORC2 activity.
Sternal defect reconstruction using a double-barrel vascularized free fibula flap: a case report

Total and subtotal sternectomy oncological defects can result in large deficits in the chest wall, disrupting the biomechanics of respiration. Reviewing the current literature involving respiratory function and rib motion after sternectomy, autologous rigid reconstruction was determined to provide the optimal reconstructive option. We describe a novel technique for sternal defect reconstruction utilizing a double-barrel, longitudinally oriented, vascularized free fibula flap associated with rib titanium plates fixation. Our reconstructive approach was able to deliver a physiological reconstruction, providing rigid support and protection while allowing articulation with adjacent ribs and preservation of chest wall mechanics.
External, Internal, and Perceived Training Loads and Their Relationships in Youth Basketball Players Across Different Positions.

PURPOSE To quantify external, internal, and perceived training loads and their relationships in youth basketball players across different playing positions. METHODS Fourteen regional-level youth male players (age: 15.2 [0.3] y) were monitored during team-based training sessions across 10 in-season weeks. The players were monitored with BioHarness-3 devices, to measure external (Impulse Load, in Newtons per second) and internal (summated-heart-rate zones [SHRZ], in arbitrary units [AU]) loads, and with the session rating of perceived exertion (sRPE, in AU) method to quantify perceived training load. Multiple linear mixed models were performed to compare training loads between playing positions (backcourt and frontcourt). Repeated-measures correlations were performed to assess the relationships between the load models, for all players and within playing positions. RESULTS External load (backcourt: 13,599 [2260] N·s; frontcourt: 14,934 [2173] N·s) and sRPE (backcourt: 345 [132] AU; frontcourt: 505 [158] AU) were higher in the frontcourt (P < .05, effect size: moderate), while SHRZ was similar between positions (backcourt: 239 [45] AU; frontcourt: 247 [43] AU) (P > .05; effect size: trivial). The correlations were as follows: large between the external load and SHRZ (r = .57, P < .001), moderate between SHRZ and sRPE (r = .45, P < .001), and small between the external load and sRPE (r = .26, P = .02). The correlation magnitudes were equivalent for external load-SHRZ (large) and SHRZ-sRPE (moderate) across positions, but different for the external load-sRPE correlation (small in backcourt; moderate in frontcourt). CONCLUSIONS In youth basketball, small-large commonalities were found between the training dose (external load) and players' responses (internal and perceived loads). Practitioners should carefully manage frontcourt players' training loads because they accumulate greater external and perceived loads than backcourt players do.
Investigations of the role of peroxisomes in sterol biosynthesis in the slime mould Dictyostelium discoideum

Dictyostelium discoideum is a good model organism to study a variety of cellular processes. Its complete genome sequence is known (dictybase.org). It has a unique life style, with motile unicellular and multicellular stages, and multiple cell types (Annesley and Fisher 2009). It is widely used to study chemotactic motility and cytoskeletal dynamics. It is also used for studying molecular pathogenesis and treatment of human disease. Furthermore, since Dictyostelium cells readily take up drugs, it has led to identification of drug targets. For instance, farnesyl diphosphate synthase was found, by use of D. discoideum, to be the primary target of bisphosphonate drugs that are widely used to prevent and treat osteoporosis. A major challenge with this organism is the difficulty of making targeted mutations by homologous recombination. It is difficult to generate targeting constructs because of the high AT contents (77.4%) of its genome. Introduction of the Clustered Regularly Interspaced Short Palindromic Repeats system (CRISPR) into D. discoideum for obtaining gene knockouts would therefore be potentially most helpful and here I report on our progress in setting this up. All previous investigations of the intracellular location of the first four enzymes involved in sterol biosynthesis from farnesyl diphosphate (FDP) have found that they locate to the ER membrane in eukaryotic cells. However, we provide strong evidence that these enzymes are peroxisomal in D. discoideum. The first step in the pathway is catalysed by squalene synthase SQS. Surprisingly, (DdSQS) contains a typical peroxisomal targeting signal type 1 (PTS1). All known PTS1-containing proteins are localized to the peroxisomal matrix whereas membrane proteins use a different pathway. However, we found that DdSQS behaves as a membrane protein. Interestingly, as in other organisms, the DdSQS has a C-terminal amino acid sequence potentially forming a hydrophobic helix but which in D. discoideum is located immediately upstream of the PTS1. Deletion of this helix does not affect peroxisomal targeting but does affect DdSQS association with the membrane and may therefore serve as a tail anchor. Furthermore, the helix plays an important role in forming a SQS homodimer. SQS is the first example of a peroxisomal membrane protein that makes use of the PTS1 pathway for its localization. We have shown that the first four enzymes of sterol biosynthesis from FDP are associated with the peroxisomal membrane by using structured illumination microscopy. This is a relatively new technique that allows imaging beyond the resolution limit for light microscopy. Furthermore, the topology of the enzymes with respect to the peroxisomal membrane was experimentally determined. We provide a model of how sterol biosynthesis from FDP takes place in the peroxisomes of D. discoideum.