Miracle-dz/UniFAR-FTUs huggingface dataset:
To be or not to be: regulation of restriction–modification systems and other toxin–antitoxin systems

One of the simplest classes of genes involved in programmed death is that containing the toxin–antitoxin (TA) systems of prokaryotes. These systems are composed of an intracellular toxin and an antitoxin that neutralizes its effect. These systems, now classified into five types, were initially discovered because some of them allow the stable maintenance of mobile genetic elements in a microbial population through postsegregational killing or the death of cells that have lost these systems. Here, we demonstrate parallels between some TA systems and restriction–modification systems (RM systems). RM systems are composed of a restriction enzyme (toxin) and a modification enzyme (antitoxin) and limit the genetic flux between lineages with different epigenetic identities, as defined by sequence-specific DNA methylation. The similarities between these systems include their postsegregational killing and their effects on global gene expression. Both require the finely regulated expression of a toxin and antitoxin. The antitoxin (modification enzyme) or linked protein may act as a transcriptional regulator. A regulatory antisense RNA recently identified in an RM system can be compared with those RNAs in TA systems. This review is intended to generalize the concept of TA systems in studies of stress responses, programmed death, genetic conflict and epigenetics.
Needle length control and the secretion substrate specificity switch are only loosely coupled in the type III secretion apparatus of Shigella

The type III secretion apparatus (T3SA), which is evolutionarily and structurally related to the bacterial flagellar hook basal body, is a key virulence factor used by many Gram-negative bacteria to inject effector proteins into host cells. A hollow extracellular needle forms the injection conduit of the T3SA. Its length is tightly controlled to match specific structures at the bacterial and host-cell surfaces but how this occurs remains incompletely understood. The needle is topped by a tip complex, which senses the host cell and inserts as a translocation pore in the host membrane when secretion is activated. The interaction of two conserved proteins, inner-membrane Spa40 and secreted Spa32, respectively, in Shigella, is proposed to regulate needle length and to flick a type III secretion substrate specificity switch from needle components/Spa32 to translocator/effector substrates. We found that, as in T3SAs from other species, substitution N257A within the conserved cytoplasmic NPTH region in Spa40 prevented its autocleavage and substrate specificity switching. Yet, the spa40N257A mutant made only slightly longer needles with a few needle tip complexes, although it could not form translocation pores. On the other hand, Δspa32, which makes extremely long needles and also formed only few tip complexes, could still form some translocation pores, indicating that it could switch substrate specificity to some extent. Therefore, loss of needle length control and defects in secretion specificity switching are not tightly coupled in either a Δspa32 mutant or a spa40N257A mutant.
ESHRE PGD Consortium/Embryology Special Interest Group--best practice guidelines for polar body and embryo biopsy for preimplantation genetic diagnosis/screening (PGD/PGS).

In 2005, the European Society for Human Reproduction and Embryology (ESHRE) Preimplantation Genetic Diagnosis (PGD) Consortium published a set of Guidelines for Best Practice to give information, support and guidance to potential, existing and fledgling PGD programmes (Thornhill AR, De Die-Smulders CE, Geraedts JP, Harper JC, Harton GL, Lavery SA, Moutou C, Robinson MD, Schmutzler AG, Scriven PN et al. ESHRE PGD Consortium best practice guidelines for clinical preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS). Hum Reprod 2005;20:35-48. ). The subsequent years have seen the introduction of a number of new technologies as well as the evolution of current techniques. Additionally, in light of ESHRE's recent advice on how practice guidelines should be written and formulated, the Consortium believed it was timely to revise and update the PGD guidelines. Rather than one document that covers all of PGD as in the original publication, these guidelines are separated into four new documents that apply to different aspects of a PGD programme; Organization of a PGD centre, fluorescence in situ hybridization-based testing, amplification-based testing and polar body and embryo biopsy for preimplantation genetic diagnosis/screening (PGD/PGS). Here we have updated the sections that pertain to embryology (including cryopreservation) and biopsy of embryos prior to PGD or PGS. Topics covered in this guideline include uses of embryo biopsy, laboratory issues relating to biopsy, timing of biopsy, biopsy procedure and cryopreserving biopsied embryos.
A qualitative inquiry on drivers of COVID-19 vaccine hesitancy among adults in Kenya

COVID-19 vaccination rates have been low among adults in Kenya (36.7% as of late March 2023) with vaccine hesitancy posing a threat to the COVID-19 vaccination program. This study sought to examine facilitators and barriers to COVID-19 vaccinations in Kenya. We conducted a qualitative cross-sectional study in two purposively selected counties in Kenya. We collected data through 8 focus group discussions with 80 community members and 8 in-depth interviews with health care managers and providers. The data was analyzed using a framework approach focusing on determinants of vaccine hesitancy and their influence on psychological constructs. Barriers to COVID-19 vaccine uptake were related to individual characteristics (males, younger age, perceived health status, belief in herbal medicine, and the lack of autonomy in decision making among women ‐ especially in rural settings), contextual influences (lifting of bans, myths, medical mistrust, cultural and religious beliefs), and COVID-19 vaccine related factors (fear of unknown consequences, side-effects, lack of understanding on how vaccines work and rationale for boosters). However, community health volunteers, trusted leaders, mandates, financial and geographic access influenced COVID-19 vaccine uptake. These drivers of hesitancy mainly related to psychological constructs including confidence, complacency, and constraints. Vaccine hesitancy in Kenya is driven by multiple interconnected factors. These factors are likely to inform evidence-based targeted strategies that are built on trust to address vaccine hesitancy. These strategies could include gender responsive immunization programs, appropriate messaging and consistent communication that target fear, safety concerns, misconceptions and information gaps in line with community concerns. There is need to ensure that the strategies are tested in the local setting and incorporate a multisectoral approach including community health volunteers, religious leaders and community leaders.
Micro-costing from healthcare professional’s perspective and acceptability of cutaneous leishmaniasis diagnostic tools in Morocco: A mixed-methods study

In Morocco, cutaneous leishmaniasis (CL) represents a concern with three causative parasite species. Despite this, rapid diagnostic test (RDT) for CL is not part of the national control strategy. This study evaluates the acceptability and micro-costing of the CL Detect Rapid Test by Inbios International. The study was conducted from June 2019 to January 2020 and included 46 healthcare professionals from 40 primary healthcare centers and district labs. Data was collected by self-administered questionnaires and interviews and analysed using NVivo, Jamovi, and Python to generate a predictive model and sensitivity analysis by calculating the average Cost-Benefit Ratio for compared CL diagnostic scenarios. The exchange rate is 1 USD = 9.6 MAD (Moroccan Dirham) in November 2019. The CL-RDT received notable acceptance for its user-friendliness and time efficiency compared to traditional microscopy. Micro-costing data revealed that the average unit cost for microscopy is 15 MAD [7–31], whereas 75 MAD [52–131] for CL-RDT. Altogether, the diagnostic cost for microscopy is 115 MAD±4, marginally higher than the 102 MAD±2 for CL-RDT (p = 0,05). Sensitivity analysis identified the most cost-benefit scenarios based on a Cost-Benefit Ratio (CBR). The optimal approach involves using CL-RDT once at a primary healthcare centre (PHC) (CBR = 1.4), especially if the unitary cost is below 79 MAD. The second-best option is using CL-RDT once at a laboratory (CBR = 1.0), which is advantageous if priced under 54 MAD. However, using CL-RDT twice for the same lesion had a less favourable CBR of 0.6 and was only beneficial if priced below 09 MAD. The reference scenario was a single CL-RDT at the PHC followed by microscopy at a laboratory. In conclusion, the forthcoming CL-RDT, expected to feature enhanced sensitivity, is advocated for deployment in resource-limited endemic areas.
Clinical significance of putative markers of cancer stem cells in gastric cancer: A retrospective cohort study

Cancer stem cells (CSCs) are thought as the source of tumor maintaining and many CSCs markers have been identified. Regarding the heterogeneity in gastric cancer (GC), TNM stage is not enough to accurately predict the prognosis. The aim of this study was to investigate the clinical significance of CSCs markers (Lgr5, Oct4, CD133, EpCAM, CD54 and Sox2) and establish a new model based on these markers to accurately predict prognosis of GC. We retrospectively enrolled 377 GC tissues from January 2006 to October 2012 to perform immunohistochemistry (IHC), and 93 pairs of GC tissues and corresponding adjacent normal gastric tissues to perform quantitative PCR (qPCR) from December 2011 to October 2012. The clinicopathological and follow-up characteristics were collected. In IHC, Oct4, CD133 and EpCAM were independently related to tumor progression, while Sox2 were associated with well or moderate differentiation (all p<0.05). Cox regression showed that Oct4-EpCAM was an independently prognostic factor, indicating that double low expression of Oct4-EpCAM group had significantly better prognosis than control group (p=0.035). Regarding qPCR, CD133 was an independent prognostic factor, showing that the prognosis of patients with CD133 high expression was significantly worse than that of patients with CD133 low expression (p<0.001). The prognostic prediction accuracy of nomogram based on Oct4-EpCAM expression in IHC was significantly better than TNM stage alone (p=0.003). Low expressions of Oct4-EpCAM in IHC and CD133 in qPCR were favorable prognostic factors in GC. The nomogram based on Oct4-EpCAM was valuable in prognostic prediction of GC patients.
Electrocardiographic Profile of Oral Piperazine Citrate in Healthy Volunteers

The electrocardiographic (ECG) profile of oral piperazine citrate was determined in healthy volunteers. Piperazine caused reduction in heart rate in all the subjects. The highest percentage of change was 15.7. The average pretreatment (73.6 ± 6.59 beats/min) when compared with the heart rate 1 hour after piperazine was administered (64.6 ± 5.21 beats/min) was statistically significant (P = 0.0054). The QT and JT intervals had average increases of 9.7% and 11.1%, respectively. In contrast, piperazine did not have any effect on the QRS complex following its administration. However, the average PR interval 1 hour after ingesting oral piperazine 2 g was significantly prolonged, 0.18 ± 0.0063 seconds compared with a pretreatment average of 0.16 ± 0.0098 seconds. The difference between the 2 values was statistically significant (P = 0.0161). No dysrhythmic phenomena were seen. Sinus rhythm was maintained in all the volunteers, with every QRS-T complex preceded by a P wave. The direction and magnitude of the mean electric axis of QRS complex and T wave were not altered by piperazine. It is concluded that oral piperazine citrate induced some changes on the ECG profile of healthy human volunteers, typical of many potent antiarrhythmic agents.
The effect of cooperator recognition on competition among clones in spatially structured microbial communities

In spatially structured microbial communities, clonal growth of stationary cells passively generates clusters of related individuals. This can lead to stable cooperation without the need for recognition mechanisms. However, recent research suggests that some biofilm-forming microbes may have mechanisms of kin recognition. To explore this unexpected observation, we studied the effects of different types of cooperation in a microbial colony using spatially explicit, agent-based simulations of two interacting strains. We found scenarios that favor a form of kin recognition in spatially structured microbial communities. In the presence of a “cheater” strain, a strain with greenbeard cooperation was able to increase in frequency more than a strain with obligate cooperation. This effect was most noticeable in high density colonies and when the cooperators were not as abundant as the cheaters. We also studied whether a polychromatic greenbeard, in which cells only cooperate with their own type, could provide a numerical benefit beyond a simple, binary greenbeard. We found the greatest benefit to a polychromatic greenbeard when cooperation is highly effective. These results suggest that in some ecological scenarios, recognition mechanisms may be beneficial even in spatially structured communities.
ON SOME COMMENSAL SHRIMPS FOUND IN THE WESTERN REGION OF SAGAMI BAY

From the coast of ]apan a few Pontoniid shrimps which are living com・ mensally in the mantle cavity of bivalve shells have hitherto been recorded, such as Conchodytes nitρonesis (de HAAN), C. iridacnae PETERS, Anchistus misakiensis YOKOY A and A. ρeclinis KEMP. Among these species, only two, C. nitρonensis and A. misakiensis are known from Sagami Bay. Recently the author obtained four Pontoniid and an Alpheid species of shrimps from the western region of Sagami Bay, in the vicinity of the Mana. zuru Marine Biological Laboratory (Text.fig. 1). Among these species, four are the commensals of bivalve shells, while the remaining one is to my inter. ests found as a commensal of a hermit crab. The present papar deals with the study of morphological features and habitat of these five species, three of which are new to science: Fam. Palaemonidae Subfam. pontoniinae Conchodytes niρonensis (de HAAN) Plaiytontonia tterostreae new species Anchistusρectinis KEMP Paranchistus s ρondylis new species Fam. Alpheidae Aretoρsis manazuruensis new species The specimens of these shrimps are deposited in the Manazuru Marine Biological Laboratory (Manazuru M. B. L.). Before going further the author wishes to express his thanks to Dr. Tune Sakai, President of the Carcinological Society of ]apan, for his kind super. vision for this study. The author also wishes to thank the late Dr. Itsuo Kubo, Professor of the Tokyo University of Fisheries for his invaluable advice and encouragements. His thanks are also due to Mr. Kensaku Muraoka of
Visual analysis of global hemorrhagic fever with renal syndrome research from 1980 to 2022: Based on CiteSpace and VOSviewer

Objective: The development and current state of hemorrhagic fever with renal syndrome (HFRS) over the past 40 years are analyzed in this study, along with explored and discovered the hotspots and frontiers in the field, which serve as the foundation for future investigation. Methods: CiteSpace and VOSviewer analysis software were used to visually analyze the literature data on HFRS from 1980 to 2022, including the annual number of publications, countries and research institutions, authors, co-cited literature and keywords. Results: The number of pertinent papers published in the field of HFRS displayed an overall upward trend from 1980 to 2022. The United States, China, Germany, Sweden, and France are the top 5 countries in terms of publishing volume, with high intermediate centrality mainly concentrated in Europe and the United States. The top 10 co-occurring keywords were hemorrhagic fever, renal syndrome, infection, virus, epidemic, nephropathia epidemical, disease, hantavirus, outbreak, and transmission. According to keyword cluster analysis, there were 4 main research fields. In the HFRS-related study, there were mainly 21 notable keywords and “Korean hemorrhagic fever” had the highest hemorrhagic value (28.87). Conclusion: The United States, China, Germany, Sweden and other countries attached great importance to the HFRS-related research. Moreover, the collaboration between authors and institutions in various collaborator clusters should be strengthened. In recent decades, investigations have focused on the study of viral infection and the clinical symptoms and pathophysiology of HFRS. Future research may concentrate on factors affecting host population distribution and density, such as vaccine development and meteorological factors pertaining to virus transmission.
Scan time reduction for readout‐segmented EPI using simultaneous multislice acceleration: Diffusion‐weighted imaging at 3 and 7 Tesla

Readout‐segmented echo‐planar imaging (rs‐EPI) can provide high quality diffusion data because it is less prone to distortion and blurring artifacts than single‐shot echo‐planar imaging (ss‐EPI), particularly at higher resolution and higher field. Readout segmentation allows shorter echo‐spacing and echo train duration, resulting in reduced image distortion and blurring, respectively, in the phase‐encoding direction. However, these benefits come at the expense of longer scan times because the segments are acquired in multiple repetitions times (TRs). This study shortened rs‐EPI scan times by reducing the TR duration with simultaneous multislice acceleration.
Glycerol Supplementation Enhances L. reuteri’s Protective Effect against S. Typhimurium Colonization in a 3-D Model of Colonic Epithelium

The probiotic effects of Lactobacillus reuteri have been speculated to partly depend on its capacity to produce the antimicrobial substance reuterin during the reduction of glycerol in the gut. In this study, the potential of this process to protect human intestinal epithelial cells against infection with Salmonella enterica serovar Typhimurium was investigated. We used a three-dimensional (3-D) organotypic model of human colonic epithelium that was previously validated and applied to study interactions between S. Typhimurium and the intestinal epithelium that lead to enteric salmonellosis. Using this model system, we show that L. reuteri protects the intestinal cells against the early stages of Salmonella infection and that this effect is significantly increased when L. reuteri is stimulated to produce reuterin from glycerol. More specifically, the reuterin-containing ferment of L. reuteri caused a reduction in Salmonella adherence and invasion (1 log unit), and intracellular survival (2 log units). In contrast, the L. reuteri ferment without reuterin stimulated growth of the intracellular Salmonella population with 1 log unit. The short-term exposure to reuterin or the reuterin-containing ferment had no observed negative impact on intestinal epithelial cell health. However, long-term exposure (24 h) induced a complete loss of cell-cell contact within the epithelial aggregates and compromised cell viability. Collectively, these results shed light on a potential role for reuterin in inhibiting Salmonella-induced intestinal infections and may support the combined application of glycerol and L. reuteri. While future in vitro and in vivo studies of reuterin on intestinal health should fine-tune our understanding of the mechanistic effects, in particular in the presence of a complex gut microbiota, this the first report of a reuterin effect on the enteric infection process in any mammalian cell type.
The socioeconomic impact of the COVID-19 lockdown on families affected by childhood respiratory illnesses in Cape Town, South Africa

The COVID-19 pandemic impacted families globally, directly and indirectly. Children presenting with respiratory illnesses are affected by emerging health systems and socioeconomic changes in the COVID-19 era. We explored the socioeconomic impacts of the COVID-19 lockdown on families with a respiratory illness diagnosed in their child in Cape Town, South Africa. This study was nested in a prospective observational cohort of children presenting with respiratory symptoms presumptive of COVID-19. We conducted 21 semi-structured interviews to explore the socioeconomic impact of the COVID-19 pandemic on families with a child affected by respiratory illnesses. We used case descriptive analysis and thematically organised common and divergent experiences. We found that socioeconomic challenges in low-income communities were exacerbated: 1) loss of pre-COVID sources of income (loss of income, employment and working hours), 2) shrinking employment opportunities due to business closures and strict preventative measures, 3) family network dependence to cope with financial pressures, 4) impact on education, implicating additional pressures due to lack of resources for adequate home schooling and 5) caregivers’ mental health and wellbeing being impacted, causing stress and anxiety due to loss of income. This study shows that the COVID-19 lockdown impacted the socioeconomic aspects of families caring for a child with a respiratory illness. Care became more complicated and adversely impacted the family’s emotional well-being and health-seeking behaviour. These impacts should be more carefully considered in order to strengthen health services and global health messaging in future pandemics.
Physical activity of older children and adolescents in Germany – Results of the HBSC study 2022 and trends since 2009/10

Background Physical activity is central to health, beginning in childhood and adolescence, and regular monitoring provides important information for strategic decisions on promoting physical activity in Germany. Methods The current survey cycle of the Health Behaviour in School-aged Children (HBSC) study gives an insight into the prevalence of the indicators daily recommended physical activity, high and low physical activity, and sporting activity among students aged between 11 and 15 for 2022. In addition, the data is compared to the survey cycles of the 2009/10, 2013/14, and 2017/18 school years and analysed over time. Results The results of the current survey cycle show that 10.8 % of girls, 20.9 % of boys, and 12.4 % of gender diverse adolescents fulfil the daily physical activity recommendation. There are also major gender-specific differences for the other indicators. The group of gender diverse adolescents needs to be analysed further. The changes over time between 2009/10 and 2022 are relatively small. While girls’ physical activity habits decreased slightly for the various indicators between 2009/10 and 2022, boys’ prevalence remained relatively stable over the same period. Conclusions Overall, in part due to the effects of the various COVID-19 lockdowns, the need for effective and population-based measures to promote physical activity in childhood and adolescence remains high.