Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Signature of Information Transfer Complexity in Cellular Membrane Proteomes

Cell membrane proteins play crucial roles in the cell's molecular interaction with its environment and within itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, and enzymes. Membrane proteomes of cellular organisms reveal some characteristics in their global topological distribution according to their evolutionary positions, and show their own information transfer complexity. Predicted transmembrane segments (TMSs) in membrane proteomes with HMMTOP showed near power-law distribution and frequency characteristics in 6-TMS and 7-TMS proteins in prokaryotes and eukaryotes, respectively. This reaffirms the important roles of membrane receptors in cellular communication and biological evolutionary history.
Site‐directed mutagenesis in bread and durum wheat via pollination by cas9/guide RNA‐transgenic maize used as haploidy inducer

Site-directed mutagenesis facilitates the experimental validation of gene function and can speed up plant breeding by producing new genetic variability or by reproducing previously known gene variants in other than their original genetic backgrounds. However, its application is challenging in wheat owing to high genomic redundancy and highly genotype-dependent DNA transfer methods (Koeppel et al., 2019). In wheat, large chromosomal regions are hardly amenable to meiotic recombination, which limits the potential for trait improvements.
Identification of the four most common β‐globin gene mutations in Greek β‐thalassemic patients and carriers by PCR‐SSCP: advantages and limitations of the method

In the present study we investigated whether the single‐strand conformational polymorphism (SSCP) method could be employed to identify (rather than simply detect) the four most common β‐globin gene mutations in the Greek population: IVS‐I‐110, Cd39, IVS‐I‐1, and IVS‐I‐6. Using DNA from 50 β‐thalassemic patients and carriers, we amplified by PCR the appropriate 238‐bp region of the human β‐globin gene, analyzed the reaction products by nondenaturing polyacrylamide gel electrophoresis, and visualized the bands by silver staining. Single‐stranded DNA (ssDNA) fragments showed a reproducible pattern of bands that was characteristic of the mutations present. With the use of control samples containing six of the 10 possible combinations of the four most common β‐globin gene mutations, we were able to predict the mutations present in a quarter of the patients studied. Our predictions were confirmed independently by the amplification refractory mutation system (ARMS) method. We conclude that this non‐radioactive PCR‐SSCP method can be used to reliably identify mutations in patients, provided that suitable controls are available. Moreover, the method is easy to apply to the identification of mutations in carriers, which makes it particularly useful for population screening. J. Clin. Lab. Anal. 20:1–7, 2006. © 2006 Wiley‐Liss, Inc.
Effects of Combined Resistance and Power Training on Cognitive Function in Older Women: A Randomized Controlled Trial

The present study compared the effects of traditional resistance training (TRT) and combined power training (PT) and TRT (PTRT) on cognitive parameters and serum brain-derived neurotrophic factor (BDNF) levels in non-demented, well-functioning, community-dwelling older women. Forty-five older women were randomized into one of three experimental groups: TRT, PTRT, and control group (CG). Cognitive tests explored global cognitive function, short-term memory, and dual-task performance. Serum BDNF levels were assessed at baseline and after the intervention. Exercise sessions were performed twice a week over 22 weeks. In TRT, exercise sessions were based on three sets of 8–10 repetitions at “difficult” intensity. In PTRT, the first session was based on PT (three sets of 8−10 repetitions at “moderate” intensity), while the second session was similar to the TRT. Our analyses indicated that overall cognitive function, short-term memory, and dual-task performance were similarly improved after TRT and PTRT. Serum BDNF concentrations were not altered by any training protocol. In conclusion, the two RT programs tested in the present trial improved global cognitive function, short-term memory and dual task performance in non-demented, well-functioning, community-dwelling older women. In addition, our findings suggest that mechanisms other than BDNF may be associated with such improvements.
Phylogenetic relationships of Dalmatinella fluviatilis Radoman, 1973 (Caenogastropoda:Rissooidea)

Morphology of Dalmatinella fluviatilis Radoman, 1973, a putative endemite of the Zrmanja River (Croatia), was checked. Shell, radula, and soft part anatomy were considered. In both male and female genitalia D. fluviatilis resembled Anagastina and Radomaniola. Molecular phylogeny, inferred from the mitochondrial cytochrome oxidase subunit I (COI) and nuclear 18S rRNA gene partial sequences, confirmed morphological observations: the sister taxa of Dalmatinella being Graecoarganiella, Radomaniola and Anagastina, and Dalmatinella belonging to the Sadlerianinae.
Sexual norms and the intention to use healthcare services related to female genital cutting: A qualitative study among Somali and Sudanese women in Norway

Background Female Genital Cutting (FGC) is a traditionally meaningful practice in Africa, the Middle East, and Asia. It is associated with a high risk of long-term physical and psychosexual health problems. Girls and women with FGC-related health problems need specialized healthcare services such as psychosexual counseling, deinfibulation, and clitoral reconstruction. Moreover, the need for psychosexual counseling increases in countries of immigration where FGC is not accepted and possibly stigmatized. In these countries, the practice loses its cultural meaning and girls and women with FGC are more likely to report psychosexual problems. In Norway, a country of immigration, psychosexual counseling is lacking. To decide whether to provide this and/or other services, it is important to explore the intention of the target population to use FGC-related healthcare services. That is as deinfibulation, an already available service, is underutilized. In this article, we explore whether girls and women with FGC intend to use FGC-related healthcare services, regardless of their availability in Norway. Methods We conducted 61 in-depth interviews with 26 Somali and Sudanese participants with FGC in Norway. We then validated our findings in three focus group discussions with additional 17 participants. Findings We found that most of our participants were positive towards psychosexual counseling and would use it if available. We also identified four cultural scenarios with different sets of sexual norms that centered on getting and/or staying married, and which largely influenced the participants’ intention to use FGC-related services. These cultural scenarios are the virgin, the passive-, the conditioned active-, and the equal- sexual partner scenarios. Participants with negative attitudes towards the use of almost all of the FGC-related healthcare services were influenced by a set of norms pertaining to virginity and passive sexual behavior. In contrast, participants with positive attitudes towards the use of all of these same services were influenced by another set of norms pertaining to sexual and gender equality. On the other hand, participants with positive attitudes towards the use of services that can help to improve their marital sexual lives, yet negative towards the use of premarital services were influenced by a third set of norms that combined norms from the two aforementioned sets of norms. Conclusion The intention to use FGC-related healthcare services varies between and within the different ethnic groups. Moreover, the same girl or woman can have different attitudes towards the use of the different FGC-related healthcare services or even towards the same services at the different stages of her life. These insights could prove valuable for Norwegian and other policy-makers and healthcare professionals during the planning and/or delivery of FGC-related healthcare services.
Detection of a Novel, and Likely Ancestral, Tn916-Like Element from a Human Saliva Metagenomic Library

Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human saliva metagenome using a functional metagenomic approach. We identified a tetracycline-resistant clone, TT31, the sequencing of which revealed it to encode both tet(M) and tet(L). Comparison of the TT31 sequence with the accessory, regulation, and recombination modules of other Tn916-like elements indicated that a partial Tn916-like element encoding a truncated orf9 was cloned in TT31. Analysis indicated that a previous insertion within the truncated orf9 created the full length orf9 found in most Tn916-like transposons; demonstrating that orf9 is, in fact, the result of a gene fusion event. Thus, we hypothesise that the Tn916-like element cloned in TT31 likely represents an ancestral Tn916.
Management of resistance to pesticides in cotton pests

Abstract In recent years, nationwide insecticide resistance management (IRM) strategies in Zimbabwe, Egypt and Australia have successfully overcome existing resistance problems on cotton and prevented further outbreaks in some key pests. These strategies, which rely heavily on pragmatic assumptions regarding the efficacy of counter‐measures and the biology of the pest, relate little to theoretical models of resistance management whose tenets have so far not been experimentally appraised. These IRM strategies are compared with a simple but rigid programme used throughout Francophone countries of Africa that has successfully controlled the pest complex on cotton and increased yield without eliciting resistance in any pests. We examine the motivations, philosophies and logistics of these control programmes on cotton, and outline scope for improvements to existing and future IRM.
The perceived impact of isoniazid resistance on outcome of first-line rifampicin-throughout regimens is largely due to missed rifampicin resistance

Background Meta-analyses on impact of isoniazid-resistant tuberculosis informed the World Health Organization recommendation of a levofloxacin-strengthened rifampicin-based regimen. We estimated the effect of initial rifampicin resistance (Rr) and/or isoniazid resistance (Hr) on treatment failure or relapse. We also determined the frequency of missed initial and acquired Rr to estimate the impact of true Hr. Methods Retrospective analysis of 7291 treatment episodes with known initial isoniazid and rifampicin status obtained from individual patient databases maintained by the Damien Foundation Bangladesh over 20 years. Drug susceptibility test results were confirmed by the programme’s designated supra-national tuberculosis laboratory. To detect missed Rr among isolates routinely classified as Hr, rpoB gene sequencing was done randomly and on a sample selected for suspected missed Rr. Results Initial Hr caused a large recurrence excess after the 8-month regimen for new cases (rifampicin for two months), but had little impact on rifampicin-throughout regimens: (6 months, new cases; 3.8%; OR 0.8, 95%CI:0.3,2.8; 8 months, retreatment cases: 7.3%, OR 1.8; 95%CI:1.3,2.6). Rr was missed in 7.6% of randomly selected "Hr" strains. Acquired Rr was frequent among recurrences on rifampicin-throughout regimens, particularly after the retreatment regimen (31.9%). It was higher in mono-Hr (29.3%; aOR 3.5, 95%CI:1.5,8.5) and poly-Hr (53.3%; aOR 10.2, 95%CI 4.4,23.7) than in susceptible tuberculosis, but virtually absent after the 8-month new case regimen. Comparing Bangladesh (low Rr prevalence) with a high Rr prevalence setting,true Hr corrected for missed Rr caused only 2–3 treatment failures per 1000 TB cases (of whom 27% were retreatments) in both. Conclusions Our analysis reveals a non-negligible extent of misclassifying as isoniazid resistance of what is actually missed multidrug-resistant tuberculosis. Recommending for such cases a “strengthened” regimen containing a fluoroquinolone provokes a direct route to extensive resistance while offering little benefit against the minor role of true Hr tuberculosis in rifampicin-throughout first-line regimen.
The Main Structural and Functional Characteristics of Photosystem-II-Enriched Membranes Isolated from Wild Type and cia3 Mutant Chlamydomonas reinhardtii

Photosystem II (PSII)-enriched membranes retain the original PSII architecture in contrast to PSII cores or PSII supercomplexes, which are usually isolated from Chlamydomonas reinhardtii. Here, we present data that fully characterize the structural and functional properties of PSII complexes in isolated PSII-enriched membranes from C. reinhardtii. The preparations were isolated from wild-type (WT) and CAH3-deficient mutant cia3 as the influence of CAH3 on the PSII function was previously proposed. Based on the equal chlorophyll content, the PSII-enriched membranes from WT and cia3 have the same amount of reaction centers (RCs), cytochrome b559, subunits of the water-oxidizing complex, Mn ions, and carotenes. They differ in the ratio of other carotenoids, the parts of low/intermediate redox forms of cytochrome b559, and the composition of outer light-harvesting complexes. The preparations had 40% more chlorophyll molecules per RC compared to higher plants. Functionally, PSII-enriched membranes from WT and cia3 show the same photosynthetic activity at optimal pH 6.5. However, the preparations from cia3 contained more closed RCs even at pH 6.5 and showed more pronounced suppression of PSII photosynthetic activity at shift pH up to 7.0, established in the lumen of dark-adapted cells. Nevertheless, the PSII photosynthetic capacities remained the same.
Endoscopic Submucosal Dissection of Papillary Gastric Adenocarcinoma; Systematic Review

This study evaluated the possibility of endoscopic submucosal dissection (ESD) for early gastric cancer with papillary adenocarcinoma (EGC-PAC). PAC, an uncommon pathologic type of stomach cancer, is classified into differentiated-type histology. However, aggressive features, including a high rate of submucosal invasion, lymphovascular invasion (LVI), and lymph node metastasis (LNM), have been reported in studies with surgical specimens. Treatment outcomes of ESD for EGC-PAC have not been precisely demonstrated. Core databases were sought for the following inclusion criteria: studies of endoscopic resection or surgery of EGC-PAC presenting the following therapeutic indicators; en bloc resection, complete resection, curative resection, recurrence, complications associated with procedures, LVI, or LNM that enabled an analysis of ESD possibility. Overall, 15 studies were included for systematic review. Frequent submucosal invasion and high LVI were noted in EGC-PAC. However, PAC was not significantly associated with LNM. Pooled en bloc resection, complete resection, and curative resection rates were 89.7% (95% confidence interval: 55.3%–98.4%), 85.3% (67.7%–94.2%), and 67% (43%–84.5%), respectively. No LNM was observed if EGC-PAC satisfied the curative resection criteria. ESD seems technically feasible, although a high LVI rate results in a lower rate of curative resection.
Bone degradation, burial medium and species representation : Debunking the myths, an experiment-based approach

Abstract This paper investigates the process of diagenesis in mammal, bird and fish bone after burial of fresh and freshly cooked specimens in selected soil types for 7 years. Almost all soft tissue had disappeared, but fur, feathers and hoof survived in acidic soil. Examination revealed that the rate of bone loss and modification could not be simply related to soil pH and/or inferred Eh; very different bone preservation occurred in geographically adjacent soils of similar pH and drainage. Bone modification also varied greatly between animals of similar size, with bird bone appearing to be particularly resilient. The state of the remains prior to burial was critically important. While boiling clearly accelerated diagenesis, other forms of cooking did not appear to have this effect. The role of micro-organisms in the degradation process is addressed. It is suggested that routine methods of bone quantification may be inappropriate for such diagenetically altered assemblages.
An effect of zinc on M-phase and G1 of the plant cell cycle in the synchronous TBY-2 tobacco cell suspension

An analysis was undertaken of the effects of a toxic metal, zinc, on plant cell suspension cultures of the TBY-2 cell line of tobacco {Nicotians tabacum cv. Bright Yellow 2) in order to determine whether Zn acts in a cell cycle-specific manner. In the control treatment (0 Zn), following a 24 h synchronization with aphidicolin and 7 h after the release from the inhibitor, the mitotic index peaked at 45%. The inclusion of Zn in the 24 h aphidicolin treatment (100, 200 or 300 ftM Zn) resulted in a concentration-dependent decrease in the mitotic peak to 30%, 22% and 10%, respectively, but did not affect the timing of the peak. Hence, despite high concentrations of Zn, cells traversed from S-phase to mitosis, albeit in smaller proportions, at the same rate as the controls. Cells treated with 0, 100 or 200 fiM Zn during synchronization and then released into Zn-free media showed successive peaks in mitotic index at 7 h and 21 h following release, i.e. Zn-treated cells progressed through a complete cell cycle at the same rate as the controls. Synchronization and subsequent release into Zn-containing medium (100 fiM) examined the effect of the metal on predominantly late G1 cells. In this treatment, the mitotic index peaked at 7 h and 19 h, indicating a slightly faster cell cycle (12 h) compared with the control (14 h). Continuous exposure to 100 fiM Zn through both synchronization and release resulted in a cell cycle of 11 h and a differential effect on the component phases: M-phase lengthened (1.5 h to 3.5 h) and G1 shortened (6 h to 1 h) compared with the control treatment. Vital staining (Evans Blue) revealed that cell mortality increased from 2.7% (0 Zn) to 6.1% and 6.5% at 100 and 200 ftM Zn, respectively. The Zn content of cells increased 40-fold from 0 to 100 fiM Zn. The data are consistent with the effects of Zn reducing the cycling cell population primarily through cell arrest rather than cell death, but also reveal that a substantial population of TBY-2 cells progressed through the cell cycle despite accumulating Zn. In particular, the duration of G2 and S-phase was remarkably invariant, clearly indicating that once plant cells meet the requirements of late G1 check-points, they are committed to divide, even in the presence of toxic concentrations of Zn. The synchronous TBY-2 cell suspension, which lacks the heterogeneity and developmental constraints of plant meristems, is an excellent system to study the effects of known toxic metals, and indeed other environmental factors, on the plant cell cycle.
Predicting Neural Response Latency of the Human Early Visual Cortex from MRI-Based Tissue Measurements of the Optic Radiation

Abstract Although the non-invasive measurement of visually evoked responses has been extensively studied, the structural basis of variabilities in latency in healthy humans is not well understood. We investigated how tissue properties of optic radiation could predict interindividual variability in the latency of the initial visually evoked component (C1), which may originate from the primary visual cortex (V1). We collected C1 peak latency data using magnetoencephalography (MEG) and checkerboard stimuli, and multiple structural magnetic resonance imaging (MRI) data from 20 healthy subjects. While we varied the contrast and position of the stimuli, the C1 measurement was most reliable when high-contrast stimuli were presented to the lower visual field (LVF). We then attempted to predict interindividual variability in C1 peak latency in this stimulus condition with a multiple regression model using MRI parameters along the optic radiation. We found that this model could predict >20% of variance in C1 latency, when the data were averaged across the hemispheres. The model using the corticospinal tract did not predict variability in C1 latency, suggesting that there is no evidence for generalization to a non-visual tract. In conclusion, our results suggest that the variability in neural latencies in the early visual cortex in healthy subjects can be partly explained by tissue properties along the optic radiation. We discuss the challenges of predicting neural latency using current structural neuroimaging methods and other factors that may explain interindividual variance in neural latency.
Apolipoprotein L-1 renal risk variants form active channels at the plasma membrane driving cytotoxicity

Recently evolved alleles of Apolipoprotein L-1 (APOL1) provide increased protection against African trypanosome parasites while also significantly increasing the risk of developing kidney disease in humans. APOL1 protects against trypanosome infections by forming ion channels within the parasite, causing lysis. While the correlation to kidney disease is robust, there is little consensus concerning the underlying disease mechanism. We show in human cells that the APOL1 renal risk variants have a population of active channels at the plasma membrane, which results in an influx of both Na+ and Ca2+. We propose a model wherein APOL1 channel activity is the upstream event causing cell death, and that the activate-state, plasma membrane-localized channel represents the ideal drug target to combat APOL1-mediated kidney disease.
Contribution of paramedics in primary and urgent care: a systematic review

Background Within the UK, there are now opportunities for paramedics to work across a variety of healthcare settings away from their traditional ambulance service employer, with many opting to move into primary care. Aim To provide an overview of the types of clinical roles paramedics are undertaking in primary and urgent care settings within the UK. Design and setting A systematic review. Method Searches were conducted of MEDLINE, CINAHL, Embase, the National Institute for Health and Care Excellence, the Journal of Paramedic Practice, and the Cochrane Database from January 2004 to March 2019 for papers detailing the role, scope of practice, clinician and patient satisfaction, and costs of paramedics in primary and urgent care settings. Free-text keywords and subject headings focused on two key concepts: paramedic and general practice/primary care. Results In total, 6765 references were screened by title and/or abstract. After full-text review, 24 studies were included. Key findings focused on the description of the clinical role, the clinical work environment, the contribution of paramedics to the primary care workforce, the clinical activities they undertook, patient satisfaction, and education and training for paramedics moving from the ambulance service into primary care. Conclusion Current published research identifies that the role of the paramedic working in primary and urgent care is being advocated and implemented across the UK; however, there is insufficient detail regarding the clinical contribution of paramedics in these clinical settings. More research needs to be done to determine how, why, and in what context paramedics are now working in primary and urgent care, and what their overall contribution is to the primary care workforce.