bluuebunny/crossref_metadata_2025 huggingface dataset:
Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum–strigosum–littorale Complex
Authors: Kawaguchi Yawako W , Tsuchikane Yuki , Tanaka Keisuke , Taji Teruaki , Suzuki Yutaka , Toyoda Atsushi , Ito Motomi , Watano Yasuyuki , Nishiyama Tomoaki , Sekimoto Hiroyuki , Tsuchimatsu Takashi
Published: June 2023

Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than 2-fold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum–strigosum–littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.
O-214 interaction of air pollution and meteorological factors on IVF outcomes: a multicenter study in China
Authors: Wu S , Tan J , Zhang Y , Hao G , Chen X , Wu X , Haiqin R
Published: June 2023

Study question

Is there an interaction between air pollution and meteorological factors on IVF outcomes?

Summary answer

The correlation between air-pollutant exposure and IVF outcomes was modified by meteorological conditions, especially temperature and wind speed.

What is known already

Previous studies revealed associations between air-pollutant exposure and in vitro fertilization (IVF) outcomes. However, modification effects of air pollution on IVF outcomes by meteorological conditions remain elusive.

Study design, size, duration

Multicenter retrospective cohort study, 2015–2020.

Participants/materials, setting, methods

This multicenter retrospective cohort study included 15,217 women from five northern Chinese cities during 2015–2020. Daily average concentrations of air pollutants (PM2.5, PM10, O3, NO2, SO2, and CO) and meteorological factors (temperature, relative humidity, wind speed, and sunshine duration) during different exposure windows were calculated as individual approximate exposure. Generalized estimating equations and stratification models were used to assess the associations of air pollution and meteorological conditions with IVF outcomes and estimated potential interactions.

Main results and the role of chance

Exposure to PM2.5, SO2, and O3 was adversely correlated with pregnancy outcomes in fresh IVF cycles. Positive associations of wind speed and sunshine duration with pregnancy outcomes were detected. In addition, we observed that embryo transfer in spring and summer had a higher likelihood to achieve a live birth compared with winter. In stratified models, pieces of evidence of interaction between meteorological factors and air pollutants on pregnancy outcomes were detected. Negative associations of PM2.5 with clinical pregnancy were only significant at lower temperatures and wind speeds. Moreover, the effects of O3 on live birth were enhanced by higher quartiles of wind speed.

Limitations, reasons for caution

First of all, we used the data from monitoring stations to estimate the individual exposure, which was inaccurate and may introduce bias. Second, due to data limitations, this study did not discuss socio-economic factors, which were reported to be associated with spatial-temporal variations of air pollutants and reproductive outcomes.

Wider implications of the findings

Pregnant women should be advised to reduce outdoor time when the air quality was poor, particularly at lower temperatures.

Trial registration number

not applicable
P-008 Acetate ameliorates doxorubicin-induced testicular toxicity by modulating Nrf2/NFkB pathway and apoptotic signaling
Authors: Akhigbe R , Adeyemi D , Hamed M , Akhigbe T
Published: June 2023

Study question

Will acetate treatment ameliorate doxorubicin-induced testicular toxicity when used concomitantly?

Summary answer

Acetate ameliorated doxorubicin-induced testicular toxicity by modulating Nrf2/NFkB and apoptotic signaling.

What is known already

Doxorubicin is an antineoplastic agent that is effective in the management of several forms of cancers. However, a major limitation of this drug is its testicular toxicity. Studies have revealed that doxorubicin impairs male fertility by inducing testicular injury via downregulation of Nrf2 and upregulation of NFkB and apoptotic signaling. On the other hand, acetate upregulates Nrf2 and downregulates NFkB and apoptotic signaling. Yet, no study has reported the impact of acetate on doxorubicin-induced testicular toxicity.

Study design, size, duration

This is a prospective experimental study using animal model. Thirty two sexually mature litter-mate male Wistar rats of comparable weight were used for the study. The study lasted 8 weeks.

Participants/materials, setting, methods

Animals were acclimatized for two weeks, then randomized into four groups (n = 8). The control rats received 0.5mL of distilled water as vehicle p.o for 14 days, acetate-treated rats received 200 mg/kg/day of acetate p.o for 14 days, doxorubicin-treated rats received 7 mg/kg of doxorubicin i.p on day 8, while acetate + doxorubicin-treated rats received treatment as acetate-treated and doxorubicin-treated. The doses of drugs used were the Human Equivalent doses for rats.

Main results and the role of chance

Acetate ameliorated doxorubicin-induced rise in testicular activities of gamma glutamyl transferase, lactate dehydrogenase activity, and lactate levels. Also, acetate ameliorated doxorubicin-induced decline in the activities of testicular superoxide dismutase and catalase, and glutathione and Nrf2 concentrations. Acetate also alleviated doxorubicin-induced rise in testicular MPO activities, malondialdehyde, TNF-α, IL-1β, and NF-kB levels. More so, acetate ameliorated doxorubicin-induced reduction in spermatogenic indices and sperm quality, circulatory levels of FSH, LH, and testosterone, and testicular concentrations of 3β-HSD, 17β-HSD, and testosterone. These events were associated with dampening of doxorubicin-induced upregulation of Bax, caspase 3 and caspase 9 activities and doxorubicin-induced downregulation of BCl-2 by acetate.

Limitations, reasons for caution

This study was conducted in a rat model; therefore the results of the present study should be extrapolated to human with caution. Clinical trials are recommended to validate these findings.

Wider implications of the findings

The present study demonstrated the ameliorative effect of acetate treatment on doxorubicin-induced testicular toxicity. These findings provide substantive evidence of the possible protective role of acetate in doxorubicin-induced testicular toxicity.

Trial registration number

Not applicable
P-114 Abdominal obesity in Polycystic ovary syndrome patients can increase endometrial stromal cells decidualization
Authors: Shalchian Z , Taheri S , Hafezi M , Shirvanizadeh F , Nasiri N , Eftekhari yazdi P
Published: June 2023

Study question

Whether abdominal obesity can change the decidualization induction potential in PCOS patients?

Summary answer

We hypothesized that considering the inflammatory origin of abdominal obesity, it may affect decidualization potential of endometrial stromal cells (ESCs).

What is known already

Polycystic ovary syndrome (PCOS) as a chronic inflammatory disease is the most common hormonal disorder in women of reproductive age, which is often associated with subfertility or infertility due to ovulation disorders and subsequently low pregnancy rate, live birth rate and a high miscarriage rate. Inflammatory Abdominal obesity (AO) is the most common phenotype in PCOS patients, which has a high association with PCOS pathogenesis. Embryo-endometrium cross-talk has a key role in successful embryo implantation, which contains inflammatory phase (decidualization induction). Followed by inflammatory phase for pregnancy support.

Study design, size, duration

Our study population were consisting of 53 infertile women including PCOS diagnosed according to Rotterdam criteria (n = 25) and normal oogenesis women (male factor infertility) (n = 28) with in vitro fertilization (IVF) / intracytoplasmic sperm injection (ICSI) and frozen embryo transfer (FET) indication. All patients were aged 25-35 referred to Royan Institute between 1st May until 1st December in 2021 for infertility treatments.

Participants/materials, setting, methods

The embryos were subdivided into four groups: PCOS with AO, PCOS without AO, nonPCOS with AO, and nonPCOS without AO patients. The embryos from each group were single cultured up to the blastocyst stage. Their embryo condition media (ECM) were pooled and added to the culture media of healthy ESCs monolayer to investigate their effects on decidualization potential via gene and protein expression analysis and ESCs migration assay.

Main results and the role of chance

Results showed that ECM generally can improved decidualization capacity in ESCs. Morphological analysis, migration assay, protein and gene expressional analysis showed PCOS with AO had the highest decidualization potential and revealed by higher expression of decidualization markers (P ≤ 0.05). NonPCOS individuals without AO had the lowest level of both gene and protein decidualization markers (P ≤ 0.05).

Limitations, reasons for caution

Due to small sample population and the ECM volume limitation, the present study remained focused on the some main decidualization markers rather than extended study.

Wider implications of the findings

Inflammation may increase endometrial receptivity, allowing more suboptimal embryos to implant; this could explain the high rate of abortion in these cases. Controlling the inflammation in PCOS patients with AO may correct the decidualization profile of these patients.

Trial registration number

Not applicable
P-396 Modified Flare/GnRH antagonist protocol versus GnRH antagonist protocol in oocyte cryopreservation cycles
Authors: Kedem A , Avraham S , Yerushalmi G , Youngster M , Gat I , Gidoni Y , Baruchin O , Landau-Rabbi M , Barkat J , Yakkov O , Hourvitz A
Published: June 2023

Study question

Is there an advantage for modified flare/ GnRH antagonist protocol in comparison to antagonist protocol in oocyte cryopreservation cycles?

Summary answer

Modified flare/ GnRH antagonist protocol is at least as good as antagonist protocol in oocyte cryopreservation cycles, potentially improving maturity rate in subgroup of patients.

What is known already

Ultrashort flare GnRH agonist (GnRHa)/GnRH -antagonist protocol offer benefits of stimulatory effect of repeated microdose flare on endogenous FSH and the advantages of GnRH antagonist suppression, including the option to use GnRHa ovulation trigger to avoid ovarian hyperstimulation syndrome. GnRHa ovulation trigger has been associated with suboptimal response that refers to lesser than expected oocyte yield. Our research group previously demonstrated the value of GnRHa follicular challenge test (FACT) in prediction of suboptimal response assessed by post ovulation trigger LH levels and as a dynamic ovarian reserve test (not published yet).

Study design, size, duration

A retrospective, age- matched, cohort study that included all non-medical oocyte cryopreservation cycles from October 2020 to December 2021. The study group included 110 women that received modified flare/ GnRH antagonist protocol and were matched with 110 women that received antagonist protocol.

Participants/materials, setting, methods

Women in the modified flare/ GnRH antagonist protocol were administered GnRHa (Decapeptyl 0.2 mg) on day 2 to menstrual cycle followed by flexible antagonist protocol. They were compared to age matched women that received flexible antagonist protocol. In both study groups GnRHa final ovulation trigger was administered.

Main results and the role of chance

Among 110 women that underwent non-medical fertility preservation with modified Flare/GnRH antagonist protocol, in comparison to 110 women that received antagonist protocol, a reduced dosage of gonadotropins was consumed with more oocytes retrieved (14.63 vs. 13.86) and more mature oocytes cryopreserved (11.32 vs. 10.14), but differences were not significantly different. In a subgroup with more than 6 oocytes retrieved significantly more mature oocytes were cryopreserved in women that received modified flare/antagonist protocol (14.03± 0.90 vs. 11.63± 0.71, p = 0.03) in comparison to women that received antagonist protocol.

Limitations, reasons for caution

Limitations of our study are its retrospective nature and lack of information on the oocyte’s fertilization competence and pregnancy outcomes.

Wider implications of the findings

Future studies will further explore the advantages of this protocol in terms of higher oocytes maturity rate, intra cycle prediction of ovarian response and suboptimal response to GnRHa triggering.

Trial registration number

not applicable
Standardized ileal digestibility of amino acids differs among sources of bakery meal when fed to growing pigs
Authors: Stein Hans H , Adeola Olayiwola , Baidoo Samuel K , Lindemann Merlin D , Adedokun Sunday A ,   North Central Coordinating Committee on Swine Nutrition (NCCC-42), Azain M J , Carter S D , Crenshaw T D , Dilger R , Hill G M , Jha R , Kerr B J , Kim S W , Liao S , Liu Y , Miller P S , Nelssen J L , Patience J F , Shannon M S , Woyengo T , Beitz D
Published: June 2023

A multistate experiment involving universities in IL, IN, KY, and MN was conducted as a part of the research efforts by the North-Central Coordinating Committee-42 on swine nutrition. The null hypothesis that there are no differences in the standardized ileal digestibility (SID) of amino acids (AA) among different sources of bakery meal was tested. Eleven sources of bakery meal were procured from swine-producing states in the United States and each source was included in one diet as the sole source of AA. A N-free diet was prepared as well. Diets were prepared in one batch and divided into four sub-batches that were subsequently distributed to the four participating universities. At each university, diets were fed to 12 pigs that had a T- cannula installed in the distal ileum. Pigs were allotted to incomplete Latin square designs with 12 pigs and 4, 5, or 6 periods for a total of 21 replicate pigs per diet. Each period lasted 7 d with ileal digesta being collected from the cannulas on days 6 and 7. Samples were analyzed for AA and the SID of each AA was calculated. Results indicated that there were differences (P < 0.001) in the SID of all AA except Pro among the 11 sources of bakery meal. The differences in SID of AA observed in this experiment were greater than what is usually observed among sources of the same ingredient, indicating that there is more variability among sources of bakery meal than among different sources of other ingredients. This is likely a consequence of different raw materials being used in the production of different sources of bakery meal. Regardless of source of bakery meal, the AA with the least SID was Lys indicating that some of the raw materials in the product streams used to generate the bakery meals may have been overheated. Additionally, the Lys:crude protein ratio in each source of bakery meal was not a good predictor of the SID of Lys, which likely reflects the different raw materials being included in the different meals. In conclusion, the SID of AA varies among different sources of bakery meal and the SID of Lys is less than the SID of all other indispensable AA.
Dietary supplementation of Ocimum

g

ratissimum improves growth performance and immune response in broilers under high ambient temperature
Authors: Lin Ping-Hung , Chen Zheng-Wen , Liu Jer-Yuh , Ye Je-Chiuan
Published: June 2023

Ocimum gratissimum (OG) was found to have immunity boosting effect on Taiwan country chickens and broiler chickens raised in moderate ambient temperature in previous studies, and the current study investigates its potential on the growth performance, blood traits, intestinal traits, and immune responses in Ross 308 broilers raised in high ambient temperature which can induce mild heat-stress (26 to 33 ˚C, average 30 ˚C). Two hundred 1-d-old male/female chicks were randomly assigned to a control group, three OG (1 g/kg, 3 g/kg, and 5 g/kg)/basal diet groups, and one Amoxicillin group. Data collected during the experiment indicated that the weight gain increase of 1742 g/bird to 1815 g/bird comparing control to 5 g/kg OG supplementation was statistically significant. In addition, the production efficiency factor was also noticeably increased by OG, particularly in the 5 g/kg group, and the uric acid levels were decreased in the 3 and 5 g/kg OG groups (from 4.26 to 2.91 and 2.90 mg/dL, respectively), indicating heat-stress alleviation was observed. Several areas of the carcass saw desirable growth changes, including the increase of breast muscle ratio observed in the 5 g/kg OG group, an overall decrease in abdominal fat in all OG groups, as well as dimensional changes in several areas of the digestive system. Lastly, the hemaglutination, hemaglutination inhibition, and phytohemaglutinin tests indicated elevated immuno-response in all OG groups. In conclusion, OG has exhibited the ability to alleviate symptoms of mild heat-stress, leading to improvement of the digestive organ development and increase of carcass mass and mean weight gain for birds, and we find OG to be a potentially beneficial feed supplement for poultry raising in high ambient temperature conditions.
A Venus in the making? Predictions for JWST observations of the ultracool M-dwarf planet LP 890-9 c
Authors: Gomez Barrientos Jonathan , Kaltenegger Lisa , MacDonald Ryan J
Published: June 2023

The recently discovered transiting super-Earth LP 890-9 c is potentially one of the best rocky exoplanets for atmospheric characterization. Orbiting an ultracool M-dwarf at the inner edge of the habitable zone, LP 890-9 c offers a new opportunity to study the climate of rocky planets at the inner edge of the habitable zone. We investigate the molecular detectability with simulated JWST transmission spectra for five potential atmospheres of LP 890-9 c. We find that a small three-transit JWST program can infer evidence of ${\rm {H}_{2}\rm {O}}$ (at 3σ confidence) for a full runaway greenhouse scenario. Alternatively, $\rm {CO_{2}}$-dominated atmospheres resembling Venus without high-altitude terminator clouds can be identified with eight transits. However, these predictions could be complicated by the impact of clouds and/or unocculted starspots. Nevertheless, JWST observations of LP 890-9 c could provide critical insights and potentially distinguish between models of rocky planets at the inner edge of the habitable zone.
Elevational differences in migration phenology of Lazuli Buntings do not support selection-based hypotheses for protandry
Authors: Savides Kim , Rushing Clark S
Published: June 2023

Documenting and understanding sex-specific variation in migratory phenology is important for predicting avian population dynamics. In spring, males often arrive on the breeding grounds before females (protandry), though whether these patterns result from fitness benefits vs. sex-specific constraints on arrival timing remains poorly understood. Sex-specific variation in the timing of fall migration is less well-documented than in spring, in part because documenting fall departures is often limited by cryptic behaviors, lower vocalization rates, and shifting territory boundaries during this time of year. We used 2 years of high-resolution encounter data from radio-frequency identification (RFID)-equipped bird feeders to monitor the daily presence of male and female Lazuli Buntings (Passerina amoena) throughout the breeding season at a high and a low-elevation site in Cache County, Utah, USA. These encounter data were used to estimate daily arrival and departure probabilities and to investigate possible differences in migration timing in relation to sex and elevation. At low elevation, male arrival (n = 15) preceded female arrival (n = 16) by ~1 week, consistent with previous research that has documented protandry in other migratory songbirds. At high elevation, however, no significant differences were found between male (n = 19) and female arrival (n = 6). In fall, we found little difference in departure dates between elevation or sex, or between years. Our observations are most consistent with constraint-based hypotheses explaining protandry, possibly relating to sex-specific constraints operating during the nonbreeding period. We additionally emphasize the need for quantifying uncertainty in phenological estimates and importance of addressing potential differences across demographic groups.
Effects of Different Frequencies of Physical Therapy Visits on Shoulder Function After Arthroscopic Rotator Cuff Repair
Authors: Demirci Serdar , Kara Dilara , Yıldız Taha İbrahim , Eraslan Leyla , Uysal Özgün , Sevinç Ceyda , Ulusoy Burak , Gazeloğlu Ali Okan , Turgut Elif , Huri Gazi , Turhan Egemen , Düzgün İrem
Published: June 2023

Objective

There is no consensus about the optimal frequency of patient visits during the rehabilitation program after arthroscopic rotator cuff repair (ARCR). This study aimed to investigate the short- and long-term effects of high-frequency (HF) and low-frequency (LF) visits of the patients in the first 12 weeks of rehabilitation after ARCR.

Methods

This was a quasi-randomized study with 2 parallel groups. Forty-seven patients with ARCR were included in 2 different patient visit frequency protocols (HF = 23, LF = 24) in 12 weeks of postoperative rehabilitation. Patients in the HF group visited the clinic twice a week, whereas patients in the LF group visited once every 2 weeks for the first 6 weeks and once a week for the following 6 weeks. Both groups performed the same exercise protocol. Outcome measurements were pain and range of motion measured at baseline; at the 3rd, 5th, 8th, 12th, and 24th weeks; and at 1-year follow-up. Shoulder function was assessed at the 12th and 24th weeks and at 1-year follow-up with an American Shoulder and Elbow Surgeons score.

Results

There was a significant group × time interaction in pain intensity during the activity between the groups. The activity pain intensity was higher in the LF group (4.2 points) at 8 weeks post surgery than in the HF group (2.7 points) (mean difference: 1.5 points, P < .05), whereas it was similar in both groups at other time periods. The interaction term was not significant between the groups for pain intensity during rest and night through the 1-year follow-up. No group × time interactions were observed in shoulder range of motion and American Shoulder and Elbow Surgeons score over the postoperative period.

Conclusion

Both rehabilitation programs at different visit frequencies after ARCR showed similar clinical results in the long term. A supervised, controlled rehabilitation program with LF visits in the first 12 weeks after surgery can be sufficient to achieve optimal clinical results and reduce rehabilitation-related costs after ARCR.

Impact

This study highlights that LF treatment protocols under the supervision of the therapist can be adopted after the arthroscopic rotator cuff repair to achieve successful results while decreasing the treatment costs. Physical therapists should plan the treatment sessions efficiently for the compliance of the patients to the exercise treatment.

Lay Summary

If you are a patient with arthroscopic rotator cuff repair, a supervised, controlled rehabilitation program with low-frequency visits in the first 12 weeks after surgery could help you achieve the best outcome and help lower the costs of rehabilitation. A total of 3 visits in the first 6 weeks might be sufficient (once every 2 weeks). More frequent visits (1–2 visits a week) should happen 6 to 12 weeks after the surgery.
Genetic Diversity and Population Structure of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) in Turkey
Authors: Cat Ahmet , Tekin Mehmet
Published: June 2023

Stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst), is one of the most important diseases threatening wheat production both in Turkey and worldwide. However, the underlying genetic dynamics of Pst populations are not fully known in Turkey. To determine the population genetic structure and migration network among regional Pst populations, a total of 140 Pst isolates collected from six geographical regions of Turkey from 2018 to 2020 were sampled and genotyped using 21 simple sequence repeat loci. A total of 70 multilocus genotypes were identified and classified into the three major genetic groups by Bayesian assignment. The highest genotypic diversity was detected in Southeastern Anatolia, showing its critical role as one of the source populations to trigger possible stripe rust epidemics. Analysis of molecular variance revealed the highest variation (90.25%) within isolates. The migration network generated by the number of effective migrants showed that the highest migration (1.0) was determined between Southeastern Anatolia and Central Anatolia, and considerable levels of migration (>0.2) were determined among the other regions, except for the Black Sea. Linkage equilibrium ( P ≥ 0.05) was detected for many geographical regions, except for Marmara ( P = 0.00) and the Mediterranean ( P = 0.03), suggesting that reproduction of Pst populations is most likely sexual or mixed (sexual and clonal). To sum up, this is the first study on the genetic relationships and population genetic structure of the Pst population in Turkey, and these findings may provide critical information to develop management strategies for wheat stripe rust.
Streptococcus gallolyticus pasteurianus, Penicillin-Sensitive Bacteremia, Which Developed During Concommtent Amoxicillin Treatment and After an ENEMA
Authors: Novotny William E. , Dalzell William A. B. , Syed Salma
Published: June 2023

Streptococcus gallolyticus pasteurianus (SGP) is normal flora in the human bowel but is seldom a pathogen in the setting of immunocompetency. A 14-month-old healthy child instrumented with a ventriculoperitoneal shunt developed acute otitis media and had a tap water enema administered for constipation. By report, fevers persisted and clinical signs of meningitis and peritonitis appeared. After 9 days of high-dose amoxicillin therapy, increased fever prompted a blood culture, which grew penicillin-susceptible SGP. Aseptic meningitis was discovered on lumbar puncture. The ventriculoperitoneal shunt was removed and was sterile for bacterial growth. Irritability and fever quickly resolved. High-dose amoxicillin treatment was ineffective in prevention of penicillin-sensitive SGP bacteremia and development of presumed SGP meningitis. Enemas in children with constipation may predispose to infectious complications from this gut flora organism from bacterial translocation or from rectal wall perforation.
Predictors of Positive Repeat Blood Cultures in Patients With Gram-Negative Bacilli Bacteremia
Authors: Gao Daniel , Ek Juliann , George Emily , Ewing Paige , Oravec Michael , Myers Joseph P
Published: June 2023

Introduction

Bloodstream infections occur commonly in the United States and are associated with significant morbidity and mortality. Bacteremia caused by gram-positive organisms has established guidelines for the use of follow-up blood cultures (FUBCs), whereas the use of FUBCs in bacteremia due to gram-negative bacilli (GNBs) does not. One study showed that positive FUBCs were more common in gram-positive coccus bacteremia (21%) than in GNB bacteremia (6%), calling into question the overall clinical utility of using FUBCs in GNB bacteremia. We investigated the factors associated with positive FUBCs in patients with GNB bacteremia in our institution to better guide clinical practice.

Methods

We used a case-control design for this study. We included patients 18 years or older admitted to our hospitals between January 1, 2014, and December 31, 2018, for a duration of ≥24 hours and who had a positive blood culture (BC) for GNB. Cases were defined as any patient with a positive FUBC drawn ≥24 hours after the initial positive BC. Control subjects were defined as patients with a negative FUBC after an initial positive BC. Characteristics of cases and control subjects were compared using descriptive statistics. A multivariable regression model using stepwise variable selection was used to identify factors significantly associated with having a positive FUBC.

Results

We identified 70 cases meeting the inclusion criteria. We compared these 70 cases with 528 control subjects. The cases and control subjects did not differ significantly in age, sex, race, or other predefined comorbid conditions. Significant predictors for having a positive FUBC included (1) organism resistance to initial antibiotic therapy (odds ratio [OR], 3.26; P = 0.035), (2) glomerular filtration rate less than 30 mL/min (OR, 2.35; P = 0.010), (3) initial admission to critical care unit (OR, 1.72; P = 0.049), (4) central line–associated infection (OR, 3.99; P = 0.004), (5) Klebsiella group infection (OR, 2.18; P = 0.015), and (6) Serratia marcescens infection (OR, 3.53; P = 0.037). Initial discordant BC was a negative predictive factor (OR, 0.44; P = 0.018). Follow-up blood culture drawn more than 48 hours after the initial positive BC had a lower likelihood of being positive than those drawn 24 to 48 hours after the initial BC (OR, 0.59; P = 0.037).

Discussion

We identified 6 independent risk factors for positive FUBCs as delineated previously. These factors provide guidance for further research and for future guideline development. The timing of the FUBCs had a significant impact on positivity. Follow-up blood cultures in GNB bacteremia should be obtained more than 48 hours after the initial positive BC.
Ruminococcus gnavus bacteraemia showing morphological diversity on Gram staining: a case report and literature review
Authors: Hioki Tatsuya , Kataoka Kensuke , Mutoh Yoshikazu
Published: June 2023

Ruminococcus gnavus

, a Gram-positive anaerobic coccus, is a common constituent of the human gut microbiota but rarely causes any disease in humans. Herein, we report a case of

R. gnavus

bacteraemia in an immunocompromised 73-year-old man with sigmoid colon perforation.

R. gnavus

is usually reported as Gram-positive diplococci or short chains on Gram staining; however, in our patient, a blood isolate showed Gram-positive cocci in long chains, and organisms from an anaerobic subculture showed morphological diversity. This case provides insight into the morphological diversity of

R. gnavus

, which might help with the recognition of these bacteria in the preliminary identification stage on Gram staining.
Cystatin C loaded in brain-derived extracellular vesicles rescues synapses after ischemic insultin vitroandin vivo
Authors: Gui Yuqi , Kim Yohan , Brenna Santra , Wilmes Maximilian , Zaghen Giorgio , Kuchenbecker-Pöls Lennart , Voß Hannah , Gocke Antonia , Schlüter Hartmut , Schweizer Michaela , Altmeppen Hermann C. , Magnus Tim , Levy Efrat , Puig Berta
Published: June 2023

Synaptic loss is an early event in the undersupplied but not yet irreversibly injured penumbra area after an ischemic stroke. Promoting synaptic preservation in this area would likely improve functional neurological recovery. In the present study, we aimed to detect proteins involved in endogenous protection mechanisms of synapses in the penumbra after stroke and to analyse the potential beneficial effect of these candidates for a prospective stroke treatment. For this, we performed Liquid Chromatography coupled to Mass Spectrometry (LC-MS)-based proteomics of synaptosomes isolated from the ipsilateral hemispheres of mice subjected to experimental stroke at different time points (24 h, 4 and 7 days) and compared them to sham-operated mice. Proteomic analyses indicated that among the differentially expressed proteins between the two groups, cystatin C (CysC) was significantly increased at 24 h and 4 days following stroke, before returning to steady-state levels at 7 days, thus indicating a potential transient and intrinsic rescue mechanism attempt of neurons. When CysC was applied to primary neuronal cultures subjected to anin vitromodel of ischemic damage, this treatment significantly improved the preservation of synaptic structures. Notably, similar effects were observed when CysC was loaded into brain-derived extracellular vesicles (BDEVs). Finally, when CysC contained in BDEVs was administered intracerebroventricularly to stroked mice, it significantly increased the expression of synaptic markers such as SNAP25, Homer-1, and NCAM in the penumbra area compared to the group supplied with empty BDEVs. Thus, we show that CysC-loaded BDEVs promote synaptic protection after ischemic damagein vitroandin vivo, opening the possibility of a therapeutic use in stroke patients.
A screening strategy based on two zebrafish eleuthero-embryo OECD test guidelines for the hazard assessment of chemicals: case of some bisphenol substitutes
Authors: Christophe Armelle , Piccini Benjamin , Hinfray Nathalie , Chadili Edith , Maillot-Marechal Emmanuelle , Cousin Xavier , Blanc Mélanie , Charlier Thierry , Pandard Pascal , Aït-Aïssa Selim , Brion François
Published: June 2023

The use of efficient screening strategies for the hazard assessment of chemicals is a current challenge to support regulatory requirements. Herein, we combined two eleuthero-embryo assays, a refined Fish Embryo Toxicity assay (OECD TG 236) and the EASZY assay (OECD TG 250), both using transgenic (tg) (cyp19a1b:GFP). The simultaneous performance of both assays provides complementary information about the acute toxicity, developmental effects, and estrogenic activity. A refined EASZY assay is however necessary to obtain accurate EC50. In this work we compared bisphenol A (BPA) and ten of its substitutes. In the refined FET, most of the selected bisphenols were more toxic than BPA, induced developmental effects on zebrafish embryos, some being identified as teratogenic compounds (BPF, BPS-MAE, BPC Cl, 4,4’ODP), and ten of them induced GFP intensity. Endocrine activity of the BPs was further investigated in the EASZY assay at concentrations that do not affect the survival and the hatching rates or induce developmental toxicity based on the target concentrations used as previously defined in the refined FET. All bisphenols elicited an estrogenic activity with the notable exception of TCBPA. Most BPs were more estrogenic than BPA, acted as agonist ligands of zfERβ2 as shown in zebrafish-specific in vitro reporter gene assay and functional zfERs were required to induce brain aromatase. Interestingly, BPS-MAE and BPS-MPE behave as pro-estrogens as they were unable to transactivate zebrafish ERβ2in vitrobut induced brain aromatasein vivo. Overall, the implementation of the zebrafish eleuthero embryo-based screening strategy efficiently provided relevant data contributing to their environmental hazard. It also provides further evidence that bisphenols modulatecyp19a1bexpression during early brain development whom potential short and long-term adverse effects need to be addressed.

SYNOPSIS

a zebrafish eleuthero embryo-screening strategy based on OECD TGs was implemented for an efficient hazard assessment of bisphenols revealing that most of them are more toxic and/or estrogenic than BPA
Estimating Insulin Sensitivity and Beta-Cell Function from the Oral Glucose Tolerance Test: Validation of a new Insulin Sensitivity and Secretion (ISS) Model
Authors: Ha Joon , Chung Stephanie T. , Springer Max , Kim Joon Young , Chen Phil , Cree Melanie G. , Behn Cecilia Diniz , Sumner Anne E. , Arslanian Silva , Sherman Arthur S.
Published: June 2023

Efficient and accurate methods to estimate insulin sensitivity (SI) and beta-cell function (BCF) are of great importance for studying the pathogenesis and treatment effectiveness of type 2 diabetes. Many methods exist, ranging in input data and technical requirements. Oral glucose tolerance tests (OGTTs) are preferred because they are simpler and more physiological. However, current analytical methods for OGTT-derived SIand BCF also range in complexity; the oral minimal models require mathematical expertise for deconvolution and fitting differential equations, and simple algebraic models (e.g., Matsuda index, insulinogenic index) may produce unphysiological values. We developed a new ISS (Insulin Secretion and Sensitivity) model for clinical research that provides precise and accurate estimates of SI and BCF from a standard OGTT, focusing on effectiveness, ease of implementation, and pragmatism. The model was developed by fitting a pair of differential equations to glucose and insulin without need of deconvolution or C-peptide data. The model is derived from a published model for longitudinal simulation of T2D progression that represents glucose-insulin homeostasis, including post-challenge suppression of hepatic glucose production and first- and second-phase insulin secretion. The ISS model was evaluated in three diverse cohorts including individuals at high risk of prediabetes (adult women with a wide range of BMI and adolescents with obesity). The new model had strong correlation with gold-standard estimates from intravenous glucose tolerance tests and hyperinsulinemic-euglycemic clamp. The ISS model has broad clinical applicability among diverse populations because it balances performance, fidelity, and complexity to provide a reliable phenotype of T2D risk.
Immunorecognition ofStreptococcus mutanssecreted proteins protects against caries by limiting tooth adhesion
Authors: Bender Omer , Khoury Jessica , Hirsch Gal , Weinberg Evgeny , Sagy Naor , Buller Shani , Lapides-Levy Shiri , Blumer Sigalit , Bar Daniel Z.
Published: June 2023

Childhood caries, a chronic disease affecting 60–90% of children in industrialized countries, results in lesions in primary and permanent dentition, leading to hospitalizations, emergency room visits, high treatment costs, and loss of school days. It diminishes the child’s ability to learn and increases the risk of caries in adulthood. Despite multiple risk factors for caries, significant interpersonal variability unaccounted for by these factors exists. The immune system generates a personal antibody repertoire that helps maintain a balanced and healthy oral microbiome.Streptococcus mutansis a key bacterium in caries development. Utilizing mass-spectrometry, we examined whichS. mutansproteins are identified by antibodies of children with and without caries and identified a core set of proteins recognizable by the immune system of most individuals. This set was enriched with proteins enabling bacterial adhesion. To study the physiological relevance of these findings, we tested the ability of saliva to preventS. mutansadherence to tooth surfaces. Saliva from caries-free individuals, but not children with caries, was found to hinder the binding ofS. mutansto teeth. These findings delineate theS. mutansproteome targeted by the immune system and suggest that the inhibition of bacterial adherence to teeth is a primary mechanism employed by the immune system to maintain oral balance and prevent caries formation. These discoveries offer fresh insights into the immune system’s role in preserving oral health and preventing caries development. TargetingS. mutansproteins implicated in bacterial adhesion could be a promising strategy for preventing childhood caries.
Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns
Authors: Gupta Shubhangi , Gupta Deepanshu , Bhatnagar Sonika
Published: June 2023

The spread of SARS-CoV-2 virus accompanied by availability of abundant sequence data publicly, provides a window for determining the spatio-temporal patterns of viral evolution in response to vaccination. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely: pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The comparative analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across different countries from the pre-vaccination phase. The dN/dS ratios showed positive selection that increased after vaccination, and the Ti/Tv ratios decreased after vaccination. C→U and G→U were the most frequent transitions and transversions in all the countries. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Mutation rates were highest in NSP3, S, N and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. N, ORF8, ORF3a and ORF10 were under highest positive selection before vaccination. They were overtaken by E, S and NSP1 in the after vaccination as well as recent sequences, with the largest change observed in NSP1. Protein-wise dN/dS ratio was also seen to vary across the different variants.

Importance

Irrespective of the different vaccine technologies used, geographical regions and host genetics, variations in the SARS-CoV-2 genome have maintained similar patterns worldwide. To the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analysing the SARS-CoV-2 evolution patterns in response to spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.
A genome-wide overexpression screen revealsMycobacterium smegmatisgrowth inhibitors encoded by mycobacteriophage Hammy
Authors: Amaya Isabel , Edwards Kaylia , Wise Bethany M. , Bhattacharyya Ankita , Pablo Clint H. D. , Mushrush Ember , Coats Amber N. , Dao Sara , Dittmar Grace , Gore Taylor , Jarva Taiya M. , Kenkebashvili Giorgi , Rathan-Kumar Sudiksha , Reyes Gabriella M. , Watts Garrett L. , Watts Victoria Kalene , Dubrow Deena , Lewis Gabrielle , Stone Benjamin H. , Xue Bingjie , Cresawn Steven G. , Mavrodi Dmitri , Sivanathan Viknesh , Heller Danielle
Published: June 2023

During infection, bacteriophages produce diverse gene products to overcome bacterial anti-phage defenses, to outcompete other phages, and take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing 25% of the Hammy genome) capable of inhibiting growth of the host bacteriumMycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known anti-mycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Elucidation by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.
Revealing cholesterol effects on PEGylated HSPC liposomes using AF4–MALS and simultaneous small- and wide-angle X-ray scattering
Authors: Hsu Ting-Wei , Yang Ching-Hsun , Su Chun-Jen , Huang Yin-Tzu , Yeh Yi-Qi , Liao Kuei-Fen , Lin Tien-Chang , Shih Orion , Lee Ming-Tao , Su An-Chung , Jeng U-Ser
Published: June 2023

Liposome development is of great interest owing to increasing requirements for efficient drug carriers. The structural features and thermal stability of such liposomes are crucial in drug transport and delivery. Reported here are the results of the structural characterization of PEGylated liposomes via small- and wide-angle X-ray scattering and an asymmetric flow field-flow fractionation (AF4) system coupled with differential refractive-index detection, multi-angle light scattering (MALS) and dynamic light scattering. This integrated analysis of the exemplar PEGylated liposome formed from hydrogenated soy phosphatidylcholine (HSPC) with the addition of cholesterol reveals an average hydrodynamic radius (R
h) of 52 nm with 10% polydispersity, a comparable radius of gyration (R
g) and a major liposome particle mass of 118 kDa. The local bilayer structure of the liposome is found to have asymmetric electronic density profiles in the inner and outer leaflets, sandwiched by two PEGylated outer layers ca 5 nm thick. Cholesterol was found to effectively intervene in lipid chain packing, resulting in the thickening of the liposome bilayer, an increase in the area per lipid and an increase in liposome size, especially in the fluid phase of the liposome. These cholesterol effects show signs of saturation at cholesterol concentrations above ca 1:5 cholesterol:lipid molar ratio.
A new ternary derivative of the Laves phases in the Mg–Co–Ga system
Authors: Pavlyuk Nazar , Dmytriv Grygoriy , Pavlyuk Volodymyr , Ciesielski Wojciech , Rozdzynska-Kielbik Beata , Indris Sylvio , Ehrenberg Helmut
Published: June 2023

Crystal structures of MgCoGa, Mg0.74CoGa0.52 and Mg0.49CoGa0.15 phases from the Mg–Co–Ga system were investigated using single-crystal diffraction. These structures belong to the family of so-called Laves phases. Hexagonal MgCoGa crystallizes as a disordered phase within the MgZn2 structure type. The orthorhombic structure of Mg0.74CoGa0.52 is a distortion variant of MgZn2 and URe2 structure type, and the structural relation is demonstrated in terms of a Bärnighausen formalism group–subgroup transformation scheme. The structure of trigonal phase Mg0.49CoGa0.15 is strongly disordered, as is shown by the presence of adjacent atomic sites which cannot be occupied simultaneously. In Mg0.49CoGa0.15, two subcells (A and B) were obtained in a ratio of 9:1. Subcell A is closely related to MgZn2-type.