FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.

A key output of the NIH-Common Fund 4D Nucleome (4DN) project is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods, which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease. Despite this progress, results from Chromatin Tracing FISH-omics experiments are difficult to share, reuse, and subject to third-party downstream analysis due to the lack of standard specifications for data exchange.

Irrigation Regime Effects on Phenolic Composition of Portuguese Grape Varieties.

Climate change has led to increased extreme weather events, such as severe droughts and intense rainfall, with regions in Portugal, like Alentejo and Algarve, being particularly affected. Understanding the influence of water availability in the concentration of phenolic compounds in autochthonous varieties could be an important tool to know how these varieties adapt to water scarcity. This work has been carried out with the aim to analyze the profile of phenolic compounds by HPLC-DAD in four Portuguese grape varieties (Tinta Gorda, Tinta Miúda, Tinta Caiada, and Moreto), cultivated under three irrigation regimes (water comfort, moderate water deficit, and rainfed).

Assessment of Cardiac Sarcoidosis with PET/CT.

F-FDG PET with CT is an important advanced imaging modality used to assess patients with suspected or known cardiac sarcoidosis (CS). F-FDG PET is indicated for CS work-up in patients with extra-CS and abnormal screening results for cardiac involvement, patients under 60 y old presenting with unexplained high-grade atrioventricular heart block, and patients with suspected CS and idiopathic ventricular arrhythmias. In patients with established CS, serial F-FDG PET can be used to assess response to immunosuppressive therapy and long-term surveillance for reactivation of myocardial inflammation in patients with low-grade or quiescent disease.

Can acclimation of freshwater rotifers to silver nanoparticles or 5-fluorouracil influence their multi- and transgenerational effects?

Emerging chemical contaminants (ECCs) are among the major environmental threats in present century. A variety of ECCs is released into aquatic environments with little knowledge about their long-term impacts to organisms. We examined the role of acclimation of the freshwater rotifer Brachionus calyciflorus to silver nanoparticles (Ag-NPs) and 5-fluorouracil (5-FU) for determining their ability to deal with these ECCs individually and in mixtures along multiple generations.

Comprehensive Two-Dimensional Gas Chromatography with a TOF MS Detector-An Effective Tool to Trace the Signature of Grape Varieties.

Varietal volatile compounds are characteristic of each variety of grapes and come from the skins of the grapes. This work focuses on the development of a methodology for the analysis of free compounds in grapes from Trincadeira, Cabernet Sauvignon, Syrah, Castelão and Tinta Barroca from the 2021 and 2022 harvests, using HS-SPME-GC × GC-TOFMS. To achieve this purpose, a previous optimization step of sample preparation was implemented, with the optimized conditions being 4 g of grapes, 2 g of NaCl, and 2 mL of HO.

Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation.

Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms and to thereby potentially provide an understanding of the evolutionary histories of past populations. To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.

Fingerprint Recognition in Forensic Scenarios.

Fingerprints are unique patterns used as biometric keys because they allow an individual to be unambiguously identified, making their application in the forensic field a common practice. The design of a system that can match the details of different images is still an open problem, especially when applied to large databases or, to real-time applications in forensic scenarios using mobile devices. Fingerprints collected at a crime scene are often manually processed to find those that are relevant to solving the crime.

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing.

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, . To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage.

Modified Atmosphere Packaging (MAP) for Seaweed Conservation: Impact on Physicochemical Characteristics and Microbiological Activity.

Conventional conservation techniques such as drying, salting or freezing do not allow for preserving the original characteristics of seaweeds. The present work aims to study the impact of minimal processing, in particular "Modified Atmosphere Packaging" (MAP), on the physicochemical characteristics and food safety of two seaweed species, "laver" () and "sea-lettuce" (), stored at 6 °C for 15 days. Different parameters were evaluated using analytical methods, namely the composition of headspace gases, color, texture, microorganisms, and volatile organic compounds (VOCs).

Phylogeography of the red alga Gracilariopsis tenuifrons (Gracilariales) along the Brazilian coast.

Changes in the sea level during the Holocene are regarded as one of the most prevalent drivers of the diversity and distribution of macroalgae in Brazil, influenced by the emergence of the Vitória-Trindade seamount chain (VTC). Gracilariopsis tenuifrons has a wide geographic distribution along the Brazilian coast, from Maranhão state (2°48'64.3" S) to Santa Catarina state (27.

Hepatocyte apical bulkheads provide a mechanical means to oppose bile pressure.

Hepatocytes grow their apical surfaces anisotropically to generate a 3D network of bile canaliculi (BC). BC elongation is ensured by apical bulkheads, membrane extensions that traverse the lumen and connect juxtaposed hepatocytes. We hypothesize that apical bulkheads are mechanical elements that shape the BC lumen in liver development but also counteract elevated biliary pressure.

The United States Supreme Court ruling and women's reproductive rights - A position statement issued by The European Board and College of Obstetrics and Gynaecology (EBCOG).

The judicial review by the Supreme Court of the United States on Roe v. Wade has fundamentally limited the ability of women to exercise choice and control of their sexual and reproductive rights in the United States. The global organisations are concerned that there remains a risk that women's rights will be diminished globally in future.

Brazilian marine phylogeography: A literature synthesis and analysis of barriers.

In the last 30 years a plethora of phylogeography studies have been published targeting Brazilian marine species. To date, several historical and extant physical and ecological processes have been identified as drivers of allopatric, sympatric and parapatric population genetic differentiation detected along the Brazilian coast. Examples of extant physical barriers include the split of the South Equatorial Current into the Brazil and North Brazil boundary currents, the mouth of major rivers (e.

The consequences of armed conflict on the health of women and newborn and sexual reproductive health - A position statement by the European Board and College of Obstetrics and Gynaecology (EBCOG).

Armed conflict brings about significant health-related consequences to the non-combatant population especially the elderly, women, and children. The consequences for women extend further than battle-related deaths. One important consequence of conflict is the population displacement resulting from individuals and families seeking safety in non-conflict zones.

Phylogeography of Colpomenia sinuosa (Ectocarpales, Phaeophyceae) along the Brazilian coast.

Colpomenia sinuosa is a cosmopolitan brown macroalgal species complex and hence a great candidate for evolutionary studies in the marine environment. Since 2009, three major C. sinuosa phylogenetic lineages, subdivided into eight subgroups, have been identified based on cox3 DNA sequences from worldwide collections.

Challenging Obstetrical Management in Generalized Peritonitis during Pregnancy.

Acute abdomen in pregnancy represents a diagnostic and therapeutic challenge, despite the current advances in modern medicine, since the typical symptoms and altered laboratory parameters mimic normal pregnancy. Acute appendicitis is the most common nonobstetric surgical emergency during pregnancy, with an incidence of 1 per 500-2000 pregnancies. Delayed diagnosis and reluctance to operate on a pregnant woman predispose to adverse maternal and fetal outcomes.

A Mathematical Model of the Dynamics of Cytokine Expression and Human Immune Cell Activation in Response to the Pathogen .

Cell-based mathematical models have previously been developed to simulate the immune system in response to pathogens. Mathematical modeling papers which study the human immune response to pathogens have predicted concentrations of a variety of cells, including activated and resting macrophages, plasma cells, and antibodies. This study aims to create a comprehensive mathematical model that can predict cytokine levels in response to a gram-positive bacterium, by coupling previous models.

Individual and mixed effects of anticancer drugs on freshwater rotifers: A multigenerational approach.

Human population growth has led to an increased release of chemical contaminants into aquatic environments. Emerging chemical contaminants (ECCs) are of increasing concern because they can affect non-target organisms in aquatic ecosystems. The application of anticancer drugs is increasing because of enhanced cancer rates and use of chemotherapy.

Expanding the phenotype of NUP85 mutations beyond nephrotic syndrome to primary autosomal recessive microcephaly and Seckel syndrome spectrum disorders.

Primary autosomal recessive microcephaly and Seckel syndrome spectrum disorders (MCPH-SCKS) include a heterogeneous group of autosomal recessive inherited diseases characterized by primary (congenital) microcephaly, the absence of visceral abnormalities, and a variable degree of cognitive impairment, short stature and facial dysmorphism. Recently, biallelic variants in the nuclear pore complex (NPC) component nucleoporin 85 gene (NUP85) were reported to cause steroid-resistant nephrotic syndrome (SRNS). Here, we report biallelic variants in NUP85 in two pedigrees with an MCPH-SCKS phenotype spectrum without SRNS, thereby expanding the phenotypic spectrum of NUP85-linked diseases.

Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians.

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe.

Struma ovarii in bilateral ovarian teratoma-case report and literature review.

Struma ovarii is an uncommon ovarian tumour, defined by the finding of thyroid tissue in the ovary, and more frequently found in teratomas. Symptoms of struma ovarii are nonspecific. The definite diagnosis is made by histological examination.

EBCOG position statement - Simulation-based training for obstetrics and gynaecology during the COVID-19 pandemic.

The specialty of Obstetrics and Gynaecology has been on the forefront of introducing simulation in post graduate education for the past two decades. Simulation training is known to enhance psychomotor skills and is considered an important step in the transition from classroom learning to clinical practice. Training on simulators allows trainees to acquire basic skills before getting involved in day to day care in real life situations.

Effects of metal nanoparticles on freshwater rotifers may persist across generations.

Nanotechnology has become one of the fastest growing industries in the current century because nanomaterials (NMs) are present in an ever-expanding range of consumer products increasing the chance of their release into natural environments. In this study, the impacts of two metal nanoparticles (Ag-NPs and CuO-NPs) and their equivalent ionic forms (Ag and Cu) were assessed on the lentic freshwater rotifer Brachionus calyciflorus and on its ability to adapt and recover through generations. In our study, Ag-NPs and CuO-NPs inhibited the rotifer population growth rate and caused mortality at low concentrations (< 100 μg L).

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.

There is a need for methods that can image chromosomes with genome-wide coverage, as well as greater genomic and optical resolution. We introduce OligoFISSEQ, a suite of three methods that leverage fluorescence in situ sequencing (FISSEQ) of barcoded Oligopaint probes to enable the rapid visualization of many targeted genomic regions. Applying OligoFISSEQ to human diploid fibroblast cells, we show how four rounds of sequencing are sufficient to produce 3D maps of 36 genomic targets across six chromosomes in hundreds to thousands of cells, implying a potential to image thousands of targets in only five to eight rounds of sequencing.