Miracle-dz/UniFAR-FTUs huggingface dataset:
Carryover effect of atrazine and its metabolite—from treated bovine spermatozoa to the embryo's transcriptome†

Abstract Atrazine (ATZ) is an extensively used herbicide and ubiquitous environmental contaminant. ATZ and its metabolite, diaminochlorotriazine (DACT), cause several cellular and functional alterations in spermatozoa. We aimed to examine the effect of ATZ/DACT on spermatozoon DNA integrity, fertilization competence, embryonic development, and transcriptome profile of in vitro-produced embryos derived from fertilization with pre-exposed sperm. Bovine spermatozoa exposed to ATZ (0.1 or 1 µM) or DACT (1 or 10 µM) during in vitro capacitation were used for in vitro fertilization of untreated oocytes. Cleavage and blastocyst-formation rates were evaluated 42 h and 7 days postfertilization, respectively. The association between DNA fragmentation and apoptosis (annexin V kit) was determined. Fertilization competence of annexin-positive (AV+) and annexin-negative (AV–) spermatozoa was examined. Microarray analysis was performed for 7-day blastocysts. Intracytoplasmic sperm injection was performed with control (AV+, AV–) and DACT (AV+, AV–) spermatozoa. Cleavage rates did not differ between groups and blastocyst formation tended to be higher for AV– vs. AV+ in both control and DACT groups, suggesting that acrosome reaction, rather than DNA fragmentation, underlies the reduced cleavage. Transcriptomic analysis revealed 139 and 230 differentially expressed genes in blastocysts derived from ATZ- and DACT-exposed spermatozoa, respectively, relative to controls. Proteomic analysis shown differential expression of proteins in ATZ- or DACT-treated spermatozoa, in particular proteins related to cellular processes and biological pathways. Therefore, we assume that factors delivered by the spermatozoa, regardless of DNA fragmentation, are also involved. Overall, the current study reveals a deleterious carryover effect of ATZ/DACT from the spermatozoa to the developing embryo. Summary sentence Summary sentence: Atrazine and its metabolite, diaminochlorotriazine, induce multifactorial damage in sperm, which is carried over to the embryo's transcriptome.
SARS-Cov2 variants and convalescent plasma: reality, fallacies, and opportunities.

In recent months genomic characterization of pandemic SARS-CoV-2 isolates identified viral variants that are less susceptible to neutralization by convalescent plasma (CP), vaccine-elicited plasma/sera, or SARS-CoV-2 monoclonal antibodies than earlier SARS-CoV-2 strains. In this Viewpoint, Casadevall et al. argue against the causal association made in some press articles between the emergence of SARS-CoV-2 variants and convalescent plasma use.
Mapping the scientific literature on reproductive health among transgender and gender diverse people: a scoping review

Abstract We conducted a scoping review to map the extent, range and nature of the scientific research literature on the reproductive health (RH) of transgender and gender diverse assigned female at birth and assigned male at birth persons. A research librarian conducted literature searches in Ovid MEDLINE®, Ovid Embase, the Cochrane Library, PubMed, Google Scholar, Gender Studies Database, Gender Watch, and Web of Science Core Collection. The results were limited to peer-reviewed journal articles published between 2000 and 2018 involving human participants, written in English, pertaining to RH, and including disaggregated data for transgender and gender diverse people. A total of 2197 unique citations with abstracts were identified and entered into Covidence. Two independent screeners performed a title and abstract review and selected 75 records for full-text review. The two screeners independently extracted data from 37 eligible articles, which were reviewed, collated, summarised, and analysed using a numerical summary and thematic analysis approach. The existing scientific research literature was limited in terms of RH topics, geographic locations, study designs, sampling and analytical strategies, and populations studied. Research is needed that: focuses on the full range of RH issues; includes transgender and gender diverse people from the Global South and understudied and multiply marginalised subpopulations; is guided by intersectionality; and uses intervention, implementation science, and community-based participatory research approaches. Further, programmes, practices, and policies that address the multilevel barriers to RH among transgender and gender diverse people addressed in the existing scientific literature are warranted.
Prostate Cancer Screening in Brazil: a single center experience in the public health system

ABSTRACT Purpose: Incidence and mortality of prostate cancer (PCa) are still increasing in developing countries. Limited access to the health system or more aggressive disease are potential reasons for this. Ethnic and social differences in developed countries seem to make inappropriate to extrapolate data from other centers. We aim to report the epidemiological profile of a PSA-screened population from a cancer center in Brazil. Materials and Methods: We retrospectively selected 9.692 men enrolled in a PCa prevention program, comprising total PSA level and digital rectal examination at the first appointment, associated with complementary tests when necessary. Men aged over 40 years-old were included after shared decision-making process. Prostate biopsy (TRUS) was performed when clinically suspected for PCa. After the diagnosis, patients underwent appropriate treatment. Results: TRUS was performed in 5.5% of men and PCa incidence was 2.6%. Overall ratio between number of patients who needed to be screened in order to diagnose one cancer was 38.9 patients, with 2.1 biopsies performed to diagnose a cancer. Positive predictive value (PPV) of TRUS biopsy in this strategy was 47.2%, varying from 38.5% (<50 years-old) to 60% (>80 years-old). We evidenced 70 patients (27.9%) classified as low risk tumors, 74 (29.5%) as intermediate risk, and 107 (42.6%) as high-risk disease. Conclusions: PSA-screening remains controversial in literature. In front of a huge miscegenated people and considering the big proportion of high-risk PCa, even in young men diagnosed with the disease, it is imperative to inform patients and health providers about these data particularities in Brazil.
The relationships and sensibility of wheat C:N:P stoichiometry and water use efficiency under nitrogen fertilization

A field study was conducted to investigate the variations in the carbon:nitrogen:phosphorus (C:N:P) stoichiometry of winter wheat (Triticum aestivum L.) and its relationships with wheat growth rate (r) and water use efficiency (WUE) under different rates of N fertilization. The results indicated that the growth rate and WUE of wheat signifi cantly increased with N fertilization and were strongly correlated with the N and P contents and C:N:P ratio. The C content in wheat was relatively stable, regardless of N fertilization, and the N contents were higher in the N fertilization treatments. In addition, the P contents were higher in the treatments without N fertilization, and changes in the C:P and N:P ratios mainly depended on changes in P. The response ratio of the N:P ratio in straw was higher than that of the other investigated traits and largely depended on changes in the plant P content due to N addition.
Improving the sensitivity of spin‐echo fMRI at 3T by highly accelerated acquisitions

Spin‐echo (SE) functional MRI (fMRI) can be highly advantageous compared to gradient‐echo (GE) fMRI with respect to magnetic field‐inhomogeneity artifacts. However, at 3T, the majority of blood oxygenation level‐dependent (BOLD) fMRI experiments are performed using T2∗ ‐weighted GE sequences because of their superior sensitivity compared to SE‐fMRI. The presented SE implementation of a highly accelerated GE pulse sequence therefore aims to improve the sensitivity of SE‐fMRI while profiting from a reduction of susceptibility‐induced signal dropout.
Restoration of confocal images for quantitative image analysis

Quantitative studies of three‐dimensional (3‐D) structure of microscopic objects have been made possible through the introduction of microscopic volume imaging techniques, most notably the confocal fluorescence microscope (CFM). Although the CFM is a true volume imager, its specific imaging properties give rise to distortions in the images and hamper subsequent quantitative analysis. Therefore, it is a prerequisite that confocal images are restored prior to analysis. The distortions can be divided into several categories: attenuation of areas in the image due to self‐absorption, bleaching effects, geometrical effects and distortions due to diffraction effects. Of these, absorption and diffraction effects are the most important. This paper describes a method aimed at the correction of diffraction‐induced distortions. All the steps necessary in restoring confocal images are discussed, including a novel method to measure instrumental properties on a routine basis. To test the restoration procedure an image of a fluorescent planar object was restored. The results show a considerable improvement in the z‐resolution and no ringing artefacts. The relevance of the method for image analysis is demonstrated by a comparison of results of applying 3‐D texture analysis to restored and unrestored images of a synthetic object. Furthermore, the method can be successfully applied to noisy fluorescence images of biological objects, such as interphase cell nucei.
Oligo‐2,6‐naphthylenevinylenes – New Building Blocks for the Preparation of Photoluminescent Polymeric Materials

Synthetic strategies towards appropriate symmetric and unsymmetric functionalization of the naphthalene ring are presented. By means of Knoevenagel and Wittig condensation reactions new fluorescent, differently functionalized oligo(2,6-naphthylenevinylene)s have been synthesized, the presence of terminal aldehyde or bromine substitution opening the way to the incorporation of the fluorescent trimers in a variety of polymeric materials. The effect of substituting the phenylene ring by the more bulky dialkoxynaphthalene system in arylenevinylene-type materials is studied from the structural point of view and the possibility to tune the emission color and the electron affinity through the introduction of naphthylenevinylene and cyano-substituted naphthylenevinylene units is also investigated.
Modeling of L-lactide polymerization by reactive extrusion

The kinetics of L-lactide ring-opening polymerization initiated by stannous octoate and triphenylphosphine was investigated in a batch apparatus (Haake Rheocord Mixer). Based on the experimental data, a kinetic model is developed, considering a coordination-insertion mechanism. Reactive extrusion experiments were further conducted for the same polymerization process, on a co-rotating twin screw extruder. The melted material flow and mixing was described by using the Ludovic ® commercial simulator. Based on the developed kinetic model and simulated flow of L-lactide polymerization mixture, a mathematical model of reactive extrusion process is formulated, describing the evolutions of monomer conversion and average molecular weight along the extruder. The model is predicting with a reasonable good accuracy the experimental data.
Measures of ventilation heterogeneity mapped with hyperpolarized helium‐3 MRI demonstrate a T2‐high phenotype in asthma

Hyperpolarized gas with helium (HHe‐3) MR (magnetic resonance) is a noninvasive imaging method which maps and quantifies regions of ventilation heterogeneity (VH) in the lung. VH is an important feature of asthma, but little is known as to how VH informs patient phenotypes.
Zataria Multiflora Extract could affect Metobolizable Energy and Organic Matter Digestibility of Canola Meal

This experiment was conducted to survey effect of adding different levels (0, 0.15, 0.3 ml/30ml buffered rumen fluid) of Zataria multiflora water extract (ZMWE) on canola meal (CM) degradability were studied by in vitro gas producing techniques. Gas production test with mixtures of filtered rumen liquid of three Taleshi native male cattle rumen in times of 2, 4, 6, 8, 12, 24, 48, 72 and 96 hours were performed. Chemical composition for ether extract , ash, neutral detergent fiber and acid detergent fiber were 3.4, 7.14, 33 and 22 percent, respectively. The results showed The organic matter digestibility (OMD), metabolizable energy (ME), short chain fatty acid (SCFA) and net energy for lactation (NE l ) contents of CM were 79.46 g/kg DM, 10.27 MJ/kg DM, 1.046 mmol and 5.28 MJ/kg DM, while for level 0.3 ZMWE were 41.85 g/kg DM, 3.63 MJ/kg DM, 1.047 mmol and 1.22 MJ/kg DM. (Mohammad Salamat Azar, Ramin Salamat Doust-Nobar, Yahya Asadi, Morteza Kiani Nahand, Saeid Najafyar, Bakhshali Khodaparast, Hamed Aminipur. Zataria Multiflora Extract could affect Metobolizable Energy and Organic Matter Digestibility of Canola Meal? . Journal of American Science 2011;7(7):131-134). (ISSN: 1545-1003). http://www.americanscience. org .
An updated census of the maize TIFY family

The TIFY gene family is a plant-specific gene family encoding a group of proteins characterized by its namesake, the conservative TIFY domain and members can be organized into four subfamilies: ZML, TIFY, PPD and JAZ (Jasmonate ZIM-domain protein) by presence of additional conserved domains. The TIFY gene family is intensively explored in several model and agriculturally important crop species and here, yet the composition of the TIFY family of maize has remained unresolved. This study increases the number of maize TIFY family members known by 40%, bringing the total to 47 including 38 JAZ, 5 TIFY, and 4 ZML genes. The majority of the newly identified genes were belonging to the JAZ subfamily, six of which had aberrant TIFY domains, suggesting loss JAZ-JAZ or JAZ-NINJA interactions. Six JAZ genes were found to have truncated Jas domain or an altered degron motif, suggesting resistance to classical JAZ degradation. In addition, seven membranes were found to have an LxLxL-type EAR motif which allows them to recruit TPL/TPP co-repressors directly without association to NINJA. Expression analysis revealed that ZmJAZ14 was specifically expressed in the seeds and ZmJAZ19 and 22 in the anthers, while the majority of other ZmJAZs were generally highly expressed across diverse tissue types. Additionally, ZmJAZ genes were highly responsive to wounding and JA treatment. This study provides a comprehensive update of the maize TIFY/JAZ gene family paving the way for functional, physiological, and ecological analysis.
On Dual- and Single-Process Models of Thinking

Popular dual-process models of thinking have long conceived intuition and deliberation as two qualitatively different processes. Single-process-model proponents claim that the difference is a matter of degree and not of kind. Psychologists have been debating the dual-process/single-process question for at least 30 years. In the present article, I argue that it is time to leave the debate behind. I present a critical evaluation of the key arguments and critiques and show that—contra both dual- and single-model proponents—there is currently no good evidence that allows one to decide the debate. Moreover, I clarify that even if the debate were to be solved, it would be irrelevant for psychologists because it does not advance the understanding of the processing mechanisms underlying human thinking.
Coronavirus Disease (COVID-19) Vaccination Associated Axillary Adenopathy: Imaging Findings and Follow-Up Recommendations in 23 Women.

We report 23 women with axillary adenopathy on breast imaging after recent coronavirus disease (COVID-19) vaccination. A total of 13% were symptomatic (axillary lump), 43% were undergoing screening; and 43% undergoing diagnostic imaging for other reasons. BI-RADS 2 was assigned in one woman, BI-RADS 3 in 21 (ultrasound in 4-24 weeks), and BI-RADS 4 in one. Radiologist familiarity and evidence-based guidelines are needed to avoid follow-up imaging and biopsies for reactive adenopathy after COVID-19 vaccination.
Revisiting the Safety of Prostaglandin Analog Eyelash Growth Products

Supplemental Digital Content is Available in the Text. BACKGROUND The FDA approved bimatoprost ophthalmic solution 0.03% for treatment of eyelash hypotrichosis in 2008. Consumer concern persists regarding potential side effects of this product. OBJECTIVE To identify gaps in the safety information associated with the use of prostaglandin eyelash growth products. MATERIALS AND METHODS Literature searches were performed using PubMed, Embase, and Nexis Uni databases without restriction to publication date, language, or study setting. RESULTS The literature pertaining to bimatoprost for treatment of eyelash hypotrichosis is dominated by industry-sponsored clinical trials. Study design choices create gaps in our understanding of the clinical safety of these products. CONCLUSION Because of study design choice, clinical trials of bimatoprost for eyelash growth may have systematically underreported the incidence of drug application discomfort and prostaglandin-associated periorbitopathy. The risk of increased iris pigmentation remains inadequately investigated. Consequently, there is an ongoing need to educate and monitor patients who choose to use these products.
Cytoplasmic Localization of Prostate-Specific Membrane Antigen Inhibitors May Confer Advantages for Targeted Cancer Therapies

This study uses STED fluorescence microscopy to reveal the subcellular fate of PSMA/PSMA inhibitor complexes near the molecular level, providing insights of great clinical interest and suggestive of advantageous targeted therapies. Targeted imaging and therapy approaches based on novel prostate-specific membrane antigen (PSMA) inhibitors have fundamentally changed the treatment regimen of prostate cancer. However, the exact mechanism of PSMA inhibitor internalization has not yet been studied, and the inhibitors' subcellular fate remains elusive. Here, we investigated the intracellular distribution of peptidomimetic PSMA inhibitors and of PSMA itself by stimulated emission depletion (STED) nanoscopy, applying a novel nonstandard live cell staining protocol. Imaging analysis confirmed PSMA cluster formation at the cell surface of prostate cancer cells and clathrin-dependent endocytosis of PSMA inhibitors. Following the endosomal pathway, PSMA inhibitors accumulated in prostate cancer cells at clinically relevant time points. In contrast with PSMA itself, PSMA inhibitors were found to eventually distribute homogeneously in the cytoplasm, a molecular condition that promises benefits for treatment as cytoplasmic and in particular perinuclear enrichment of the radionuclide carriers may better facilitate the radiation-mediated damage of cancerous cells. This study is the first to reveal the subcellular fate of PSMA/PSMA inhibitor complexes at the nanoscale and aims to inspire the development of new approaches in the field of prostate cancer research, diagnostics, and therapeutics. Significance: This study uses STED fluorescence microscopy to reveal the subcellular fate of PSMA/PSMA inhibitor complexes near the molecular level, providing insights of great clinical interest and suggestive of advantageous targeted therapies. Graphical Abstract: http://cancerres.aacrjournals. org/content/canres/81/8/2234/F1.large. jpg. Graphical Abstract
Role of flexural phonons in carrier mobility of two-dimensional semiconductors: free standing vs on substrate

Two-dimensional (2D) semiconductor is a promising material for future electronics. It is believed that the flexural phonon (FP) induced scattering plays an important role in the room-temperature carrier mobility, and the substrate can significantly affect such scattering. Here we develop an ‘implicit’ substrate model, which allows us to effectively quantify different effects of the substrate on the FP scattering. In conjunction with the first-principles calculations, we study the intrinsic mobilities of the holes in Sb and electrons in MoS2 as representative examples for 2D semiconductors. We find that the FP scattering is not dominant and is weaker than other scatterings such as that induced by longitudinal acoustic (LA) phonon. This is due to the significantly smaller electron–phonon-coupling (EPC) matrix elements for the FP compared with that for the LA phonon in the free-standing case; although the substrate enhances the FP EPC, it suppresses the FP population, making the FP scattering still weaker than the LA scattering. Our work improves the fundamental understanding of the role of FP and its interaction with the substrate in carrier mobility, and provides a computational model to study the substrate effects.
Associations between Early Maladaptive Schema Domains of Parents and Their Adult Children: The Role of Defense Styles.

Although existing research recognized the associations between early maladaptive schemas (EMSs) of parents and their adult children, the mechanisms that underpin these associations were not fully understood. Therefore, the purpose of the current study was to explore the role of defense styles (DSs) on the associations between two EMS domains (Disconnection/Rejection and Impaired Autonomy) of parents and their adult children. Two hundred and fifteen families (i.e., mother, father, and their adult children) participated in the study. Both parents and their adult children were asked to complete Young Schema Questionnaire-Short Form (YSQ-SF) and Defense Style Questionnaire (DSQ) to assess their EMS domains and DSs. According to the results of the current study, there were significant associations between Disconnection/Rejection and Impaired Autonomy EMS domains of parents and their adult children, and these associations were mediated by only immature DS of parents and their adult children in a serial mediation model. These results contributed to our understanding of the associations between EMS domains of parents and their adult children through immature DSs. Moreover, our findings highlighted the importance of synthesizing the concepts of different theories to enhance our understanding of mental representations in families.
A synthetic mRNA cell reprogramming method using CYCLIN D1 promotes DNA repair, generating improved genetically stable human induced pluripotent stem cells

A key challenge for clinical application of induced pluripotent stem cells (iPSC) to accurately model and treat human pathologies depends on developing a method to generate genetically stable cells to reduce long‐term risks of cell transplant therapy. Here, we hypothesized that CYCLIN D1 repairs DNA by highly efficient homologous recombination (HR) during reprogramming to iPSC that reduces genetic instability and threat of neoplastic growth. We adopted a synthetic mRNA transfection method using clinically compatible conditions with CYCLIN D1 plus base factors (OCT3/4, SOX2, KLF4, LIN28) and compared with methods that use C‐MYC. We demonstrate that CYCLIN D1 made iPSC have (a) lower multitelomeric signal, (b) reduced double‐strand DNA breaks, (c) correct nuclear localization of RAD51 protein expression, and (d) reduced single‐nucleotide polymorphism (SNP) changes per chromosome, compared with the classical reprogramming method using C‐MYC. CYCLIN D1 iPSC have reduced teratoma Ki67 cell growth kinetics and derived neural stem cells successfully engraft in a hostile spinal cord injury (SCI) microenvironment with efficient survival, differentiation. We demonstrate that CYCLIN D1 promotes double‐stranded DNA damage repair predominantly through HR during cell reprogramming to efficiently produce iPSC. CYCLIN D1 reduces general cell stress associated with significantly lower SIRT1 gene expression and can rescue Sirt1 null mouse cell reprogramming. In conclusion, we show synthetic mRNA transfection of CYCLIN D1 repairs DNA during reprogramming resulting in significantly improved genetically stable footprint in human iPSC, enabling a new cell reprogramming method for more accurate and reliable generation of human iPSC for disease modeling and future clinical applications.