Effect of prostaglandin alone and in combination with trace minerals on the follicular and luteal dynamics, estrus response and pregnancy in sub-estrus buffaloes (Bubalus bubalis)

Sub-estrus is a condition when buffaloes do not display behavioural estrus signs, despite being in estrus and causes a delay in conception and increases the service period. The present study describes the effect of synthetic prostaglandin (PGF2α) alone and in combination with trace minerals on the follicular and corpus luteum (CL) dynamics, serum estradiol (E2) and progesterone (P4) concentration correlating estrus response and pregnancy outcome in sub-estrus buffaloes during the breeding season. A total of 50 sub-estrus buffaloes, identified through ultrasonography (USG) examination, were randomly allocated into three groups, viz. T1 (Synthetic PGF2α, Inj. Cloprostenol 500 μg, i.m, n = 17), T2 (Synthetic PGF2α + Trace mineral supplementation, Inj. Stimvet 1 mL/100 kg body weight, i.m., n = 17) and control (untreated; n = 16). Following treatment, 100% of sub-estrus buffaloes were induced estrus in the T1 and T2 groups, while only 18.75% were induced in the control. The CL diameter and serum P4 concentration were significantly lower at post-treatment, whereas the pre-ovulatory follicle (POF) size and serum E2 concentration were significantly higher in the T1 and T2 groups as compared to the control (p < .05). The buffaloes of the T2 group had a greater proportion of moderate intensities estrus than those of T1. Moreover, the proportion of buffaloes conceived in the T1 and T2 were 41.2% and 52.95%, respectively. The larger POF diameter and higher serum E2 concentration were associated with intense intensity estrus and higher conception rate (66.7%) in sub-estrus buffaloes. Similarly, CL regression rate, POF size and serum E2 concentration were relatively higher in the buffaloes conceived as compared to those not conceived. It is concluded that synthetic PGF2α in combination with trace minerals induces moderate to intense intensities estrus in a greater proportion of sub-estrus buffaloes and increases the conception rate during the breeding season. Moreover, behavioural estrus attributes correlating follicle and luteal morphometry, serum E2 and P4 concentration could be used to optimise the breeding time for augmenting the conception rate in sub-estrus buffaloes.

Ensemble Detection of DNA Engineering Signatures

Synthetic biology is creating genetically engineered organisms at an increasing rate for many potentially valuable applications, but this potential comes with the risk of misuse or accidental release. To begin to address this issue, we have developed a system called GUARDIAN that can automatically detect signatures of engineering in DNA sequencing data, and we have conducted a blinded test of this system using a curated Test and Evaluation (T&E) data set. GUARDIAN uses an ensemble approach based on the guiding principle that no single approach is likely to be able to detect engineering with perfect accuracy. Critically, ensembling enables GUARDIAN to detect sequence inserts in 13 target organisms with a high degree of specificity that requires no subject matter expert (SME) review.

Proton Shell Gaps in N=28 Nuclei from the First Complete Spectroscopy Study with FRIB Decay Station Initiator

The first complete measurement of the β-decay strength distribution of _{17}^{45}Cl_{28} was performed at the Facility for Rare Isotope Beams (FRIB) with the FRIB Decay Station Initiator during the second FRIB experiment. The measurement involved the detection of neutrons and γ rays in two focal planes of the FRIB Decay Station Initiator in a single experiment for the first time. This enabled an analytical consistency in extracting the β-decay strength distribution over the large range of excitation energies, including neutron unbound states. We observe a rapid increase in the β-decay strength distribution above the neutron separation energy in _{18}^{45}Ar_{27}. This was interpreted to be caused by the transitioning of neutrons into protons excited across the Z=20 shell gap. The SDPF-MU interaction with reduced shell gap best reproduced the data. The measurement demonstrates a new approach that is sensitive to the proton shell gap in neutron rich nuclei according to SDPF-MU calculations.

A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening

Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Leveraging several recent advances, we assembled a prime editing platform capable of high-efficiency substitution editing across a set of engineered prime editing guide RNAs (epegRNAs) and corresponding target sequences (80% median intended editing). Then, using a custom library of 240,000 epegRNAs targeting >17,000 codons with 175 different substitution types, we benchmarked our platform for functional interrogation of small substitution variants (1-3 nucleotides) targeted to essential genes. Resulting data identified negative growth phenotypes for nonsense mutations targeted to ~8,000 codons, and comparing those phenotypes to results from controls demonstrated high specificity. We also observed phenotypes for synonymous mutations that disrupted splice site motifs at 3' exon boundaries. Altogether, we establish and benchmark a high-throughput prime editing approach for functional characterization of genetic variants with simple readouts from multiplexed experiments.

Forensic DNA Profiling: Legal and Ethical Considerations

Forensic DNA analysis is vital in criminal investigations, posing intricate legal and ethical dilemmas. This emphasises the need to balance DNA technology benefits with individual rights, prioritizing privacy, consent, and ethical practices. Stringent regulation of DNA data management is essential to prevent misuse and ensure privacy protection. Advances like probabilistic genotyping software improve interpretation accuracy, addressing complexities in mixture analysis. Responsible DNA use also requires navigating emerging technologies like next-generation sequencing while upholding ethical standards. Establishing transparency, accuracy, and ethical conduct throughout the analysis process is crucial for building public trust. Regulatory oversight and accountability mechanisms are necessary to address errors and maintain fairness in DNA data management. Through continuous dialogue and adherence to ethical standards, the forensic community can uphold scientific integrity and preserve public confidence in DNA analysis.

Protocol for the isolation of tumor cell-derived extracellular vesicles followed by in vivo metastasis assessment in a murine ovarian cancer model

Extracellular vesicles (EVs) play a crucial role in facilitating communication between cancer cells and their immediate or remote microenvironments, thereby promoting the extensive spread of cancer throughout the body. In this context, we present a protocol for the isolation of tumor cell-derived EVs followed by in vivo metastasis assessment in a murine ovarian cancer model. We describe steps for the isolation and characterization of EVs from ID8 cells, development of a metastatic mouse model, and sample preparation for flow cytometry. For complete details on the use and execution of this protocol, please refer to Gupta et al.1.

From Gut to Hormones: Unraveling the Role of Gut Microbiota in (Phyto)Estrogen Modulation in Health and Disease

The human gut microbiota regulates estrogen metabolism through the "estrobolome," the collection of bacterial genes that encode enzymes like β-glucuronidases and β-glucosidases. These enzymes deconjugate and reactivate estrogen, influencing circulating levels. The estrobolome mediates the enterohepatic circulation and bioavailability of estrogen. Alterations in gut microbiota composition and estrobolome function have been associated with estrogen-related diseases like breast cancer, enometrial cancer, and polycystic ovarian syndrome (PCOS). This is likely due to dysregulated estrogen signaling partly contributed by the microbial impacts on estrogen metabolism. Dietary phytoestrogens also undergo bacterial metabolism into active metabolites like equol, which binds estrogen receptors and exhibits higher estrogenic potency than its precursor daidzein. However, the ability to produce equol varies across populations, depending on the presence of specific gut microbes. Characterizing the estrobolome and equol-producing genes across populations can provide microbiome-based biomarkers. Further research is needed to investigate specific components of the estrobolome, phytoestrogen-microbiota interactions, and mechanisms linking dysbiosis to estrogen-related pathology. However, current evidence suggests that the gut microbiota is an integral regulator of estrogen status with clinical relevance to women's health and hormonal disorders.

ITPA polymorphisms do not predict additional risk beyond TPMT and NUDT15 for thiopurine-induced cytopenia in inflammatory bowel disease

INTRODUCTION AND AIM

Thiopurine-related leukopenia is associated with polymorphisms in the thiopurine methyltransferase (TPMT) and nucleoside diphosphate-linked moiety X type motif 15 (NUDT15) genes. However, those polymorphisms explain only a fraction of thiopurine-related leukopenia. Our aim was to study the role of an inosine triphosphate pyrophosphatase (ITPA) polymorphism in patients with inflammatory bowel disease (IBD) and thiopurine-related leukopenia that was unexplained by the TPMT and NUDT15 polymorphisms.

MATERIAL AND METHODS

We enrolled consecutive IBD patients on thiopurines (azathioprine or 6-mercaptopurine) from January 2019-March 2020, at a tertiary care center in North India. The presence of the ITPA (C.94C > A) polymorphism was evaluated in all patients, along with its association with thiopurine-related leukopenia.

RESULTS

Of the 33 patients (from a total of 119 patients) that developed leukopenia, 8 had the TPMT (n = 1) or NUDT15 (n = 7) polymorphism. Of the remaining 111 patients, their mean age was 36.36 ± 13.54 years and 57 (51.3%) were males. Twenty-five (21.01%) had unexplained leukopenia. The ITPA polymorphism was detected in 4 (16%) patients in the unexplained leukopenia group and 24 (27.9%) patients in the non-leukopenia group (p = 0.228). The odds ratio for predicting leukopenia with the ITPA polymorphism was 0.4921 (95% CI 0.1520-1.5830, p = 0.234).

CONCLUSION

The ITPA (C.94C > A) polymorphism was frequently detected in the study population but was not predictive for leukopenia in patients with IBD on thiopurine therapy.

A Reappraisal of the Antiviral Properties of and Immune Regulation through Dietary Phytochemicals

In the present era of the COVID-19 pandemic, viral infections remain a major cause of morbidity and mortality worldwide. In this day and age, viral infections are rampant and spreading rapidly. Among the most aggressive viral infections are ebola, AIDS (acquired immunodeficiency syndrome), influenza, and SARS (severe acute respiratory syndrome). Even though there are few treatment options for viral diseases, most of the antiviral therapies are ineffective owing to frequent mutations, the development of more aggressive strains, drug resistance, and possible side effects. Traditionally, herbal remedies have been used by healers, including for dietary and medicinal purposes. Many clinical and scientific studies have demonstrated the therapeutic potential of plant-derived natural compounds. Because of unsafe practices like blood transfusions and organ transplants from infected patients, medical supply contamination. Our antiviral therapies cannot achieve sterile immunity, and we have yet to find a cure for these pernicious infections. Herbs have been shown to improve therapeutic efficacy against a wide variety of viral diseases because of their high concentration of immunomodulatory phytochemicals (both immunoinhibitory and anti-inflammatory). Combined with biotechnology, this folk medicine system can lead to the development of novel antiviral drugs and therapies. In this Review, we will summarize some selected bioactive compounds with probable mechanisms of their antiviral actions, focusing on the immunological axis of these compounds.

Flourescence sensors for heavy metal detection: major contaminants in soil and water bodies

Due to the increasing consumption of heavy metals, there is a rising need for specific and useful methods that are employed for the detection of heavy metals. Fluorescence sensing is a highly selective, rapid and biosensing technique that is employed in the determination of some heavy metals in any sample of soil or water, any other living person, the food being consumed or any other substance which are being used daily. These fluorescent methods are a type of analytical technique and they are mainly based on detection. Many types of metal conjugated molecules have been used of the detection of these heavy metals with various mechanisms. We have taken into account some specific sensor molecules as they were more suitable and easily accessible. These techniques that were employed in the detection of various heavy metals such as copper, lead and mercury have been discussed in the following review article.

A systematic review and meta-analysis of the sources of Campylobacter in poultry production (preharvest) and their relative contributions to the microbial risk of poultry meat

A systematic review and meta-analysis were conducted to idetnify the relative contributions of the sources of Campylobacter in poultry live production to Campylobacter prevalence of broiler meat. The keywords of Campylobacter, prevalence, live production, and broiler were used in Google Scholar to address the research interest. A total of 16,800 citations were identified, and 63 relevant citations were included in the meta-analysis after applying predetermined inclusion and exclusion criteria. A generalized linear mixed model approach combined with logit transformation was used in the current meta-analysis to stabilize the variance. The analysis revealed that Campylobacter is ubiquitous in the poultry house exterior environment including surroundings, wildlife, domestic animals, and farm vehicle, with a predicted prevalence of 14%. The recovery of Campylobacter in the interior environment of the poultry house is far less abundant than in the exterior, with a prevalence of 2%, including litter, water, insects, mice, feed, and air. A lack of evidence was observed for vertical transmission due to the day-old chicks being free of Campylobacter from 4 studies identified. Live birds are the predominant carrier of Campylobacter, with a predicted prevalence of 41%. Transportation equipment used for live haul had an overall prevalence of 39%, with vehicles showing a predicted prevalence of 44% and crates with a predicted prevalence of 22%. The results of this meta-analysis highlight the need to implement effective biosecurity measures to minimize the risk of Campylobacter in poultry meat, as human activity appears to be the primary factor for Campylobacter introduction.

Study Protocol of the Bladder Adjuvant RadioTherapy (BART) Trial: A Randomised Phase III Trial of Adjuvant Radiotherapy Following Cystectomy in Bladder Cancer

AIMS

To assess the efficacy and safety of adjuvant radiotherapy in patients with high-risk muscle-invasive bladder cancer (MIBC) following radical cystectomy (RC) and chemotherapy.

MATERIALS AND METHODS

The BART (Bladder Adjuvant RadioTherapy) trial is an ongoing multicentric, randomised, phase III trial comparing the efficacy and safety of adjuvant radiotherapy versus observation in patients with high-risk MIBC. The key eligibility criteria include ≥pT3, node-positive (pN+), positive margins and/or nodal yield <10, or, neoadjuvant chemotherapy for cT3/T4/N+ disease. In total, 153 patients will be accrued and randomised, in a 1:1 ratio, to either observation (standard arm) or adjuvant radiotherapy (test arm) following surgery and chemotherapy. Stratification parameters include nodal status (N+ versus N0) and chemotherapy (neoadjuvant chemotherapy versus adjuvant chemotherapy versus no chemotherapy). For patients in the test arm, adjuvant radiotherapy to cystectomy bed and pelvic nodes is planned with intensity-modulated radiotherapy to a dose of 50.4 Gy in 28 fractions using daily image guidance. All patients will follow-up with 3-monthly clinical review and urine cytology for 2 years and subsequently 6 monthly until 5 years, with contrast-enhanced computed tomography abdomen pelvis 6 monthly for 2 years and annually until 5 years. Physician-scored toxicity using Common Terminology Criteria for Adverse Events version 5.0 and patient-reported quality of life using the Functional Assessment of Cancer Therapy - Colorectal questionnaire is recorded pre-treatment and at follow-up.

ENDPOINTS AND STATISTICS

The primary endpoint is 2-year locoregional recurrence-free survival. The sample size calculation was based on the estimated improvement in 2-year locoregional recurrence-free survival from 70% in the standard arm to 85% in the test arm (hazard ratio 0.45) using 80% statistical power and a two-sided alpha error of 0.05. Secondary endpoints include disease-free survival, overall survival, acute and late toxicity, patterns of failure and quality of life.

CONCLUSION

The BART trial aims to evaluate whether contemporary radiotherapy after standard-of-care surgery and chemotherapy reduces pelvic recurrences safely and also potentially affects survival in high-risk MIBC.

^{133}In: A Rosetta Stone for Decays of r-Process Nuclei

The β decays from both the ground state and a long-lived isomer of ^{133}In were studied at the ISOLDE Decay Station (IDS). With a hybrid detection system sensitive to β, γ, and neutron spectroscopy, the comparative partial half-lives (logft) have been measured for all their dominant β-decay channels for the first time, including a low-energy Gamow-Teller transition and several first-forbidden (FF) transitions. Uniquely for such a heavy neutron-rich nucleus, their β decays selectively populate only a few isolated neutron unbound states in ^{133}Sn. Precise energy and branching-ratio measurements of those resonances allow us to benchmark β-decay theories at an unprecedented level in this region of the nuclear chart. The results show good agreement with the newly developed large-scale shell model (LSSM) calculations. The experimental findings establish an archetype for the β decay of neutron-rich nuclei southeast of ^{132}Sn and will serve as a guide for future theoretical development aiming to describe accurately the key β decays in the rapid-neutron capture (r-) process.

Network-augmented compartmental models to track asymptomatic disease spread

Summary

A major challenge in understanding the spread of certain newly emerging viruses is the presence of asymptomatic cases. Their prevalence is hard to measure in the absence of testing tools, and yet the information is critical for tracking disease spread and shaping public health policies. Here, we introduce a framework that combines classic compartmental models with travel networks and we use it to estimate asymptomatic rates. Our platform, traSIR ("tracer"), is an augmented susceptible-infectious-recovered (SIR) model that incorporates multiple locations and the flow of people between them; it has a compartment model for each location and estimates of commuting traffic between compartments. TraSIR models both asymptomatic and symptomatic infections, as well as the dampening effect symptomatic infections have on traffic between locations. We derive analytical formulae to express the asymptomatic rate as a function of other key model parameters. Next, we use simulations to show that empirical data fitting yields excellent agreement with actual asymptomatic rates using only information about the number of symptomatic infections over time and compartments. Finally, we apply our model to COVID-19 data consisting of reported daily infections in the New York metropolitan area and estimate asymptomatic rates of COVID-19 to be ∼34%, which is within the 30-40% interval derived from widespread testing. Overall, our work demonstrates that traSIR is a powerful approach to express viral propagation dynamics over geographical networks and estimate key parameters relevant to virus transmission.

Availability and implementation

No public repository.

Leveraging protein language models for accurate multiple sequence alignments

Multiple sequence alignment (MSA) is a critical step in the study of protein sequence and function. Typically, MSA algorithms progressively align pairs of sequences and combine these alignments with the aid of a guide tree. These alignment algorithms use scoring systems based on substitution matrices to measure amino acid similarities. Although successful, standard methods struggle on sets of proteins with low sequence identity: the so-called twilight zone of protein alignment. For these difficult cases, another source of information is needed. Protein language models are a powerful new approach that leverages massive sequence data sets to produce high-dimensional contextual embeddings for each amino acid in a sequence. These embeddings have been shown to reflect physicochemical and higher-order structural and functional attributes of amino acids within proteins. Here, we present a novel approach to MSA, based on clustering and ordering amino acid contextual embeddings. Our method for aligning semantically consistent groups of proteins circumvents the need for many standard components of MSA algorithms, avoiding initial guide tree construction, intermediate pairwise alignments, gap penalties, and substitution matrices. The added information from contextual embeddings leads to higher accuracy alignments for structurally similar proteins with low amino-acid similarity. We anticipate that protein language models will become a fundamental component of the next generation of algorithms for generating MSAs.

Microsecond Isomer at the N=20 Island of Shape Inversion Observed at FRIB

Excited-state spectroscopy from the first experiment at the Facility for Rare Isotope Beams (FRIB) is reported. A 24(2)-μs isomer was observed with the FRIB Decay Station initiator (FDSi) through a cascade of 224- and 401-keV γ rays in coincidence with ^{32}Na nuclei. This is the only known microsecond isomer (1  μs≤T_{1/2}<1  ms) in the region. This nucleus is at the heart of the N=20 island of shape inversion and is at the crossroads of the spherical shell-model, deformed shell-model, and ab initio theories. It can be represented as the coupling of a proton hole and neutron particle to ^{32}Mg, ^{32}Mg+π^{-1}+ν^{+1}. This odd-odd coupling and isomer formation provides a sensitive measure of the underlying shape degrees of freedom of ^{32}Mg, where the onset of spherical-to-deformed shape inversion begins with a low-lying deformed 2^{+} state at 885 keV and a low-lying shape-coexisting 0_{2}^{+} state at 1058 keV. We suggest two possible explanations for the 625-keV isomer in ^{32}Na: a 6^{-} spherical shape isomer that decays by E2 or a 0^{+} deformed spin isomer that decays by M2. The present results and calculations are most consistent with the latter, indicating that the low-lying states are dominated by deformation.

Pan-Asian adapted ESMO Clinical Practice Guidelines for the diagnosis, staging and treatment of patients with metastatic breast cancer

The most recent version of the European Society for Medical Oncology (ESMO) Clinical Practice Guidelines for the diagnosis, staging and treatment of patients with metastatic breast cancer (MBC) was published in 2021. A special, hybrid guidelines meeting was convened by ESMO and the Korean Society of Medical Oncology (KSMO) in collaboration with nine other Asian national oncology societies in May 2022 in order to adapt the ESMO 2021 guidelines to take into account the differences associated with the treatment of MBC in Asia. These guidelines represent the consensus opinions reached by a panel of Asian experts in the treatment of patients with MBC representing the oncological societies of China (CSCO), India (ISMPO), Indonesia (ISHMO), Japan (JSMO), Korea (KSMO), Malaysia (MOS), the Philippines (PSMO), Singapore (SSO), Taiwan (TOS) and Thailand (TSCO). The voting was based on the best available scientific evidence and was independent of drug access or practice restrictions in the different Asian countries. The latter were discussed when appropriate. The aim of these guidelines is to provide guidance for the harmonisation of the management of patients with MBC across the different regions of Asia, drawing from data provided by global and Asian trials whilst at the same time integrating the differences in genetics, demographics and scientific evidence, together with restricted access to certain therapeutic strategies.

Heat ameliorative measures in Murrah buffalo (Bubalus bubalis) heifers during summer: effect on microclimate, thermal comfort, and behavior

Water buffalo (Bubalus bubalis) is the mainstay of milk production in Asian countries including India. However, the hot climate of the country remains the biggest bottleneck to exploit the potential of this species. Therefore, a study was conducted to assess the effect of heat ameliorative measures on microclimate, thermal comfort, and behavior of Murrah buffalo heifers during summer. Buffalo heifers (n = 24) between the age of 15 and 20 months with a mean body weight of 363.75 ± 11.27 kg were randomly grouped into four treatments based on their age and body weight. The heifers kept in the shed without any cooling served as CON (control), while the animals of group CJ were tied with a cooling jacket. The buffalo heifers of the CJF group were subjected to the cooling jacket with forced air ventilation, whereas the intermittent (10 min at 2-h intervals) sprinkling followed by forced air ventilation was practiced in group SF between 900 and 1800 h throughout the experiment. The microclimatic variables were low in the sheds of groups CJ, CJF, and SF than the CON. The physiological responses such as rectal temperature, skin temperature, respiration rate, and pulse rate were reduced in groups CJ, CJF, and SF than the CON at 1400 h. The serum cortisol was less in the CJF and SF than those of CON group. The animals of the CJ, CJF, and SF groups spent more time for feeding and rumination with less frequent longer bouts. The extended periods of lying followed by shorter standing and idling were observed in groups CJ, CJF, and SF when compared with the CON. It may be therefore concluded that cooling jacket and intermittent sprinkling in combination with forced air ventilation might be helpful in improving the micro-environment, thermal comfort, and behavior of buffalo heifers particularly under tropical climates during summer.

A systematic review and meta-analysis of the sources of Salmonella in poultry production (pre-harvest) and their relative contributions to the microbial risk of poultry meat

Salmonella is a major foodborne pathogen associated with poultry and poultry products and a leading cause for human salmonellosis. Salmonella is known to transmit in poultry flocks both vertically and horizontally. However, there is a lack of knowledge on relative contribution of the factors on Salmonella prevalence in poultry live production system including hatchery, feed, water, environment-interior, and -exterior. Therefore, a systematic review and meta-analysis was conducted to quantify the potential sources of Salmonella during preharvest and their relative contributions to the microbial risk of poultry meat. A total of 16,800 studies identified from Google Scholar and 37 relevant studies were included in the meta-analysis for relative contributions to Salmonella positivity on broilers after applying exclusion criteria. A generalized linear mixed model approach combined with logit transformation was used in the current study to stabilize the variance. The analysis revealed that the hatchery is the most significant contributor of Salmonella with a prevalence of 48.5%. Litter, feces, and poultry house internal environment were the other 3 major contributing factors with a prevalence of 25.4, 16.3, and 7.9%, respectively. Moreover, poultry house external environment (4.7%), feed (4.8%), chicks (4.7%), and drinker water also contributed to the Salmonella positivity. Results from this meta-analysis informed the urgent need for controls in live production to further reduce Salmonella in fresh, processed poultry. The control strategies can include eliminating the sources of Salmonella and incorporating interventions in live production to reduce Salmonella concentrations in broilers.

Monkeypox virus: phylogenomics, host-pathogen interactome and mutational cascade

While the world is still recovering from the Covid-19 pandemic, monkeypox virus (MPXV) awaits to cause another global outbreak as a challenge to all of mankind. However, the Covid-19 pandemic has taught us a lesson to speed up the pace of viral genomic research for the implementation of preventive and treatment strategies. One of the important aspects of MPXV that needs immediate insight is its evolutionary lineage based on genomic studies. Utilizing high-quality isolates from the GISAID (Global Initiative on Sharing All Influenza Data) database, primarily sourced from Europe and North America, we employed a SNP-based whole-genome phylogeny method and identified four major clusters among 628 MPXV isolates. Our findings indicate a distinct evolutionary lineage for the first MPXV isolate, and a complex epidemiology and evolution of MPXV strains across various countries. Further analysis of the host-pathogen interaction network revealed key viral proteins, such as E3, SPI-2, K7 and CrmB, that play a significant role in regulating the network and inhibiting the host's cellular innate immune system. Our structural analysis of proteins E3 and CrmB revealed potential disruption of stability due to certain mutations. While this study identified a large number of mutations within the new outbreak clade, it also reflected that we need to move fast with the genomic analysis of newly detected strains from around the world to develop better prevention and treatment methods.

Going Virtual: Adapting an Institutional Annual Bereavement Event During the COVID-19 Pandemic

Our institution's annual bereaved family event was modified to a virtual format during the COVID-19 pandemic. While necessary to comply with physical distancing directives, the transition also provided greater accessibility for families. Virtual events were feasible and appreciated by attendees. Future hybrid bereavement events should be considered to allow families more flexibility and accessibility.

Chromoblastomycosis treated with posaconazole and adjunctive imiquimod: lending innate immunity a helping hand

Chromoblastomycosis (CBM) is a difficult-to-treat, chronic fungal infection of the skin and subcutaneous tissue. The evidence base for treatment is scarce, with no standardised therapeutic approach. Chronicity of CBM infection is postulated to be due in part to a failure of host cell-mediated immunity to generate a proinflammatory response sufficient for fungal clearance. We present a case of a chronic chromoblastomycosis lesion of the hand present for nearly four decades, previously refractory to itraconazole monotherapy, that was successfully treated with a combination of posaconazole and adjunctive immunotherapy with topical Imiquimod, a toll-like receptor 7 agonist. Serial biopsies and images demonstrate the clinical and histopathological improvement of the lesion. Randomised trials of antifungal therapy with adjunctive imiquimod are warranted to determine whether a combination of antifungal and host-directed therapy improves outcomes for this neglected tropical mycosis.

Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers

Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with other molecules, alterations in the sites that participate in these interactions may be of critical importance. To uncover the extent to which these sites evolve across primates, we built a structurally-derived dataset of ~4,200 one-to-one orthologous sequence groups across 18 primate species, consisting of ~68,000 ligand-binding sites that interact with DNA, RNA, small molecules, ions, or peptides. Using this dataset, we identify functionally important patterns of conservation and variation within the amino acid residues that facilitate protein-ligand interactions across the primate phylogeny. We uncover that interaction sites are significantly more conserved than other sites, and that sites binding DNA and RNA further exhibit the lowest levels of variation. We also show that the subset of ligand-binding sites that do vary are enriched in components of gene regulatory pathways and uncover several instances of human-specific ligand-binding site changes within transcription factors. Altogether, our results suggest that ligand-binding sites have experienced selective pressure in primates and propose that variation in these sites may have an outsized effect on phenotypic variation in primates through pleiotropic effects on gene regulation.

Response assessment by positron emission tomography-computed tomography as compared with contrast-enhanced computed tomography in childhood Hodgkin lymphoma can reduce the need for radiotherapy in low- and middle-income countries

INTRODUCTION

The InPOG-HL-15-01, a multicentric prospective study, used a risk-stratified and response-based approach with doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) backbone to treat children and adolescents with newly diagnosed Hodgkin lymphoma (HL) and reduce the use of radiation therapy (RT). Children/adolescents with bulky disease or inadequate response at early response assessment (ERA) after two cycles of chemotherapy were assigned to receive RT. For ERA, positron emission tomography computed tomography (PET-CT) was recommended but not mandatory in view of limited access. This study aimed to compare the impact of using contrast-enhanced computed tomography (CECT) and PET-CT on treatment decisions and outcomes.

METHODOLOGY

396 patients were enrolled and 382 had an ERA at the assigned time point. Satisfactory response was defined as Deauville score 3 or less for patients undergoing PET-CT and complete response (CR)/very good partial response (VGPR) for patients undergoing CECT. Outcomes of interest incorporate 5 year event-free survival (EFS), EFS including abandonment (EFSa), and overall survival (OS).

RESULTS

At ERA, satisfactory response was documented in 277 out of 382 (72.5%) participants and this was significantly higher in PET-CT (151 out of 186, 81.2%) as compared with CECT-based assessments (126 out of 196, 64.3%) respectively (p value < .001). Amongst the 203 patients with nonbulky disease (wherein the indication for RT was entirely dependent on ERA), 96 out of 114 (84.2%) and 61 out of 89 (68.5%) patients achieved a satisfactory response according to the PET-CT and CECT (p value = .008) respectively and hence a lesser proportion of patients in the PET-CT arm received RT. Despite a lower usage of RT the 5 year OS of both groups, ERA based on CECT (91.8%) versus PET-CT (94.1%) was comparable (p value = .391) and so was the 5 year EFS (86.7 vs. 85.5%, p value = .724).

CONCLUSION

Use of PET-CT as the modality for ERA is more likely to indicate a satisfactory response as compared with CECT and thereby decreases the need for RT in response-based treatment algorithm for HL-afflicted children. The reduction in the application of RT did not impact the overall outcome and plausibly would lower the risk of delayed toxic effects.

Machine learning accurately quantifies epicardial adipose tissue from non-contrast CT images in coronary artery disease

Funding Acknowledgements

Type of funding sources: Other. Main funding source(s): Industry Alignment Fund – Pre-positioning Programme

Background

Epicardial adipose tissue (EAT) is the visceral fat deposit within the pericardium that surrounds the heart and the coronary arteries. EAT volume measured from non-contrast CT (NCCT) has been demonstrated to be significantly associated with adverse cardiovascular risk,1 particularly in patients with coronary artery disease.2 However, routine measurement of EAT volume is still challenging in clinical practice, as it is a tedious manual process and prone to human error.

Purpose

We aimed to develop a fully automated AI toolkit (i.e., AI EAT) for the quantification of EAT from routine NCCT scans and assess its performance in reference to clinical ground truth.

Methods

This is a multicenter study which performs CT scans in 5000 Asian Admixture patients (APOLLO study NCT05509010). In the current stage of this study, NCCT data analysis were conducted in 551 patients with 26,037 images. AI EAT was developed via a novel deep learning framework using an ensemble region-based UNet. The region-based UNet uses 2 component UNet models to perform segmentation of pericardium at the apex region and non-apex region (middle and basal). EAT volume was obtained by automated thresholding of the voxels (-190 to -30 Hounsfield Unit) within the pericardium (Figure 1). The network was trained in 501 patients with 23,712 NCCT images and tested in 50 patients with 2,325 NCCT images. The performance of AI EAT was evaluated with respect to clinical ground truth using Dice similarity coefficient (DSC), Pearson correlation, and Bland-Altman analysis.

Results

The AI EAT quantification process took less than 10 seconds per subject, compared with 20-30 minutes for expert readers. Compared to clinical ground truth, our AI EAT achieved a DSC of 0.96±0.01 and 0.91±0.02 for pericardium and EAT segmentations, respectively. There was strong agreement between the AI EAT and clinical ground truth in deriving the EAT volume (r=0.99, P&lt;0.001) with minimal error of 7±5%.

Conclusion

End-to-end deep learning system accurately quantifies epicardial adipose tissue in standard NCCT images without manual segmentation.

Results of in situ fixation of Andersson lesion by posterior approach in 35 cases

STUDY OBJECTIVE

Due to the rarity of the Andersson lesion (AL), the literature is ambiguous regarding the type of surgical fixation, need for debridement and deformity correction. The purpose of this retrospective study is to evaluate the efficacy, feasibility and functional outcome of posterior fixation in AL.

MATERIALS AND METHODS

This study included 35 patients having thoracolumbar AL operated for in situ fixation and fusion with minimum of 24-month follow-up. VAS (Visual Analogue Score) back pain, ODI (Oswestry Disability Index), Frankel's grade were compared and analyzed. Union status was noted with complications.

RESULTS

The mean age of 35 patients was 56.34(± 11.3) years with average follow-up of 51.49 months. Two patients had AL at two levels. 27/37 AL were at discal level. Average estimated blood loss (EBL) was 276.43 ml and duration of surgery was 130.43 min. On an average, operated segments needed 7.77 screws. There were ten minor complications without long-term sequel. Neurological improvement was noted in 30 patients. Average preoperative VAS score improved from 8.69 to 3.14, ODI score improved from 68.76 to 18.77 at final follow-up which were significant (p < 0.05). There was significant improvement in Frankel's grading (Z = - 4.354, P = 0.00).

CONCLUSIONS

Surgical management of AL by posterior approach and posterior stabilization can give satisfactory results without the need of extensive anterior reconstruction, bone grafting or deformity correction procedures without added morbidity and complications.

Crossing N=28 Toward the Neutron Drip Line: First Measurement of Half-Lives at FRIB

New half-lives for exotic isotopes approaching the neutron drip-line in the vicinity of N∼28 for Z=12-15 were measured at the Facility for Rare Isotope Beams (FRIB) with the FRIB decay station initiator. The first experimental results are compared to the latest quasiparticle random phase approximation and shell-model calculations. Overall, the measured half-lives are consistent with the available theoretical descriptions and suggest a well-developed region of deformation below ^{48}Ca in the N=28 isotones. The erosion of the Z=14 subshell closure in Si is experimentally confirmed at N=28, and a reduction in the ^{38}Mg half-life is observed as compared with its isotopic neighbors, which does not seem to be predicted well based on the decay energy and deformation trends. This highlights the need for both additional data in this very exotic region, and for more advanced theoretical efforts.

Neurological evolution of patients in coma at 72 hours after out-of-hospital cardiac arrest

Introduction

Establishing neurological prognosis after out-of-hospital cardiac arrest (OHCA) safely and early in those patients who remain in a coma at 72 hours of admission.

Purpose

To analyze the prognostic performance of neuron-specific enolase (NSE), Somatosensory evoked potentials (SSEPs) and electroencephalogram (EEG) in these patients.

Methods

Prospective and observational study, including all OHCAs admitted to a Cardiovascular Intensive Care Unit (CICU) of a tertiary hospital. Neurological stratification was performed at 72 hours with NSE (poor prognosis &gt;60 ng/mL), SSEP (poor prognosis in the absence of N20) and EEG (poor prognosis). The sensitivity and specificity of each test for poor prognosis were calculated, as well as the three tests together.

Results

Between 03/17/2013 and 02/24/2022, 422 OHCAs were registered, of which 170 patients remained in a coma at 72 hours. The EEG had a sensitivity of 84% and a specificity of 89% due to poor prognosis. SSEPs had a sensitivity of 68% and a specificity of 98% due to poor prognosis. The NSE had a sensitivity of 67% and a specificity of 100% due to poor prognosis. The three tests were able to be performed on 110 patients, the sensitivity for poor prognosis of the three combined tests was 49% and the specificity was 100%.

Conclusions

In patients in a coma at 72 hours of OHCA, the most specific test to establish a poor prognosis was SSEP and the most sensitive was EEG. The combination of the three had a specificity of 100%.

Funding Acknowledgement

Type of funding sources: None.

Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings

Knowledge of how proteins interact with DNA is essential for understanding gene regulation. Although DNA-binding specificities for thousands of transcription factors (TFs) have been determined, the specific amino acid-base interactions comprising their structural interfaces are largely unknown. This lack of resolution hampers attempts to leverage these data in order to predict specificities for uncharacterized TFs or TFs mutated in disease. Here we introduce recognition code learning via automated mapping of protein-DNA structural interfaces (rCLAMPS), a probabilistic approach that uses DNA-binding specificities for TFs from the same structural family to simultaneously infer both which nucleotide positions are contacted by particular amino acids within the TF as well as a recognition code that relates each base-contacting amino acid to nucleotide preferences at the DNA positions it contacts. We apply rCLAMPS to homeodomains, the second largest family of TFs in metazoans and show that it learns a highly effective recognition code that can predict de novo DNA-binding specificities for TFs. Furthermore, we show that the inferred amino acid-nucleotide contacts reveal whether and how nucleotide preferences at individual binding site positions are altered by mutations within TFs. Our approach is an important step toward automatically uncovering the determinants of protein-DNA specificity from large compendia of DNA-binding specificities and inferring the altered functionalities of TFs mutated in disease.

The influence of anastomotic techniques on postoperative anastomotic complications: Results of the Oesophago-Gastric Anastomosis Audit

BACKGROUND

The optimal anastomotic techniques in esophagectomy to minimize rates of anastomotic leakage and conduit necrosis are not known. The aim of this study was to assess whether the anastomotic technique was associated with anastomotic failure after esophagectomy in the international Oesophago-Gastric Anastomosis Audit cohort.

METHODS

This prospective observational multicenter cohort study included patients undergoing esophagectomy for esophageal cancer over 9 months during 2018. The primary exposure was the anastomotic technique, classified as handsewn, linear stapled, or circular stapled. The primary outcome was anastomotic failure, namely a composite of anastomotic leakage and conduit necrosis, as defined by the Esophageal Complications Consensus Group. Multivariable logistic regression modeling was used to identify the association between anastomotic techniques and anastomotic failure, after adjustment for confounders.

RESULTS

Of the 2238 esophagectomies, the anastomosis was handsewn in 27.1%, linear stapled in 21.0%, and circular stapled in 51.9%. Anastomotic techniques differed significantly by the anastomosis sites (P < .001), with the majority of neck anastomoses being handsewn (69.9%), whereas most chest anastomoses were stapled (66.3% circular stapled and 19.3% linear stapled). Rates of anastomotic failure differed significantly among the anastomotic techniques (P < .001), from 19.3% in handsewn anastomoses, to 14.0% in linear stapled anastomoses, and 12.1% in circular stapled anastomoses. This effect remained significant after adjustment for confounding factors on multivariable analysis, with an odds ratio of 0.63 (95% CI, 0.46-0.86; P = .004) for circular stapled versus handsewn anastomosis. However, subgroup analysis by anastomosis site suggested that this effect was predominantly present in neck anastomoses, with anastomotic failure rates of 23.2% versus 14.6% versus 5.9% for handsewn versus linear stapled anastomoses versus circular stapled neck anastomoses, compared with 13.7% versus 13.8% versus 12.2% for chest anastomoses.

CONCLUSIONS

Handsewn anastomoses appear to be independently associated with higher rates of anastomotic failure compared with stapled anastomoses. However, this effect seems to be largely confined to neck anastomoses, with minimal differences between techniques observed for chest anastomoses. Further research into standardization of anastomotic approach and techniques may further improve outcomes.

The 1, 2-ethylenediamine SQ109 protects against tuberculosis by promoting M1 macrophage polarization through the p38 MAPK pathway

Directly Observed Treatment Short-course (DOTs), is an effective and widely recommended treatment for tuberculosis (TB). The antibiotics used in DOTs, are immunotoxic and impair effector T cells, increasing the risk of re-infections and reactivation. Multiple reports suggest that addition of immune-modulators along with antibiotics improves the effectiveness of TB treatment. Therefore, drugs with both antimicrobial and immunomodulatory properties are desirable. N¹-(Adamantan-2-yl)-N²-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]ethane-1,2-diamine (SQ109) is an asymmetric diamine derivative of adamantane, that targets Mycobacterial membrane protein Large 3 (MmpL3). SQ109 dissipates the transmembrane electrochemical proton-gradient necessary for cell-wall biosynthesis and bacterial activity. Here, we examined the effects of SQ109 on host-immune responses using a murine TB model. Our results suggest the pro-inflammatory nature of SQ109, which instigates M1-macrophage polarization and induces protective pro-inflammatory cytokines through the p38-MAPK pathway. SQ109 also promotes Th1 and Th17-immune responses that inhibit the bacillary burden in a murine model of TB. These findings put forth SQ109 as a potential-adjunct to TB antibiotic therapy.

The adamantine derivative SQ109 induces protective pro-inflammatory cytokines and promotes Th1 and Th17-immune responses that inhibit bacterial burden in a tuberculosis mouse model.

P-707 RCT of Dual-Triger (GnRH-Agonist &amp; hCG) versus hCG-Trigger alone for Normal Responders in IVF-ICSI Cycles

Study question

Does Dual Triger with GnRH-Agonist with hCG in IVF-ICSI cycles in normal responders improve oocyte quality and pregnancy outcome compared to Triger with hCG alone?

Summary answer

Yes, Dual Triger with GnRH-Agonist with hCG in IVF-ICSI cycles in normal responders improve oocyte quality and pregnancy outcome compared to Triger with hCG alone.

What is known already

Dual-Triggering for final oocyte maturation combining GnRH-Agonist with hCG can improve clinical outcomes in high responders during IVF–ICSI cycles. .

However, there is insufficient evidence regarding the impact of a Dual-Trigger on the reproductive outcome in normal responders.

Some studies reported a significantly improved ongoing pregnancy rate and live-birth rate in fresh-embryo-transfer cycles for a dual-trigger group compared with the hCG-trigger group in normal responders . By contrast, several studies have demonstrated that dual trigger of oocyte maturation was not associated with a change in the live-birth rate in FET cycles for normal ovarian responders .

Study design, size, duration

RCT of 214 patients of IVF-ICSI Cycles between 2016 - 2020 were included in the study .The inclusion criteria in the study were: Age &lt; 40 years, AMH &gt;1 ng/ml, AFC : 07-20 and FSH &lt;10 IU/l.

The exclusion criteria were Poor-Ovarian-Reserve (Low-AMH &lt;1 ng/ml) and patients at high-risk of developing OHSS (High-AMH &gt;07 or AFC &gt;20). Recombinant-FSH dose was adjusted according to E2 levels and follicular monitoring along with a flexible GnRH-Antagonist-Protocol.

Participants/materials, setting, methods

RCT of 214 patients of IVF-ICSI Cycles between 2016-2020 were included in the study and were divided in two groups.

Administration of the GnRH-antagonist was initiated based on a flexible protocol and final oocyte-maturation was triggered either by hCG alone (contol group) or by combining GnRH-Agonist with hCG (2000 IU) (study group).Data on number of oocytes retrieved, number of mature (MII) oocytes, embryos and blastocysts and clinical pregnancy rate were assessed and compared.

Main results and the role of chance

The Implantation-Rate (16% versus 33%) and the Clinical-Pregnancy-Rate per patient (18% versus 38%) were significantly higher in the Dual Triger of GnRH-Agonist with hCG study group, compaired to contol group of Triger with hCG alone.

Dual-trigger approach appears superior to an hCG trigger alone with regard to the number of top-quality embryos produced.

Final oocyte maturation is the key step in ART cycles and Human-Chorionic-Gonadotropin (hCG) alone has been used for final oocyte maturation for many years and has been demonstrated to promote an increased pregnancy rate. However, the administration of hCG for final oocyte maturation results in supraphysiologic steroid levels in the luteal phase due to its long half-life and is consequently associated with an increased risk of OHSS. The hCG trigger may have negative impacts on endometrial receptivity and embryo quality .

The GnRH-Agonist trigger benefits the induction of both an FSH and an LH surge and the possibility of retrieving more mature MII oocytes than is expected with an hCG trigger . Drawback of a GnRHa trigger was LH depletion and the withdrawal of LH support of the corpus luteum , however this problem has been overcome with intensive luteal phase support (LPS) and luteal-phase hCG administration .

Limitations, reasons for caution

The present study did not include a third arm of patients who were triggered with GnRH-Agonist alone.

If we had added the third arm, we would have been able to test whether it was the administration of GnRH-Agonist or the co-administration of GnRH-Agonist and hCG that improved the outcome .

Wider implications of the findings

We conclude that using the dual trigger for final follicular maturation in normal responder increases the number of good quality mature MII oocytes and top-quality blastocysts compared to triggering with hCG alone.

The increase in the number of good quality blastocysts improved the outcome of the IVF-CSI cycle in normal responders.

Trial registration number

not applicable