Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii1[OPEN]

The zygotic wall program is executed by the heterodimeric homeobox transcription factors GSM1/GSP1 via transcriptional activation and post-transcriptional suppression in Chlamydomonas. The sexual cycle of the unicellular Chlamydomonas reinhardtii culminates in the formation of diploid zygotes that differentiate into dormant spores that eventually undergo meiosis. Mating between gametes induces rapid cell wall shedding via the enzyme g-lysin; cell fusion is followed by heterodimerization of sex-specific homeobox transcription factors, GSM1 and GSP1, and initiation of zygote-specific gene expression. To investigate the genetic underpinnings of the zygote developmental pathway, we performed comparative transcriptome analysis of both pre- and post-fertilization samples. We identified 253 transcripts specifically enriched in early zygotes, 82% of which were not up-regulated in gsp1 null zygotes. We also found that the GSM1/GSP1 heterodimer negatively regulates the vegetative wall program at the posttranscriptional level, enabling prompt transition from vegetative wall to zygotic wall assembly. Annotation of the g-lysin-induced and early zygote genes reveals distinct vegetative and zygotic wall programs, supported by concerted up-regulation of genes encoding cell wall-modifying enzymes and proteins involved in nucleotide-sugar metabolism. The haploid-to-diploid transition in Chlamydomonas is masterfully controlled by the GSM1/GSP1 heterodimer, translating fertilization and gamete coalescence into a bona fide differentiation program. The fertilization-triggered integration of genes required to make related, but structurally and functionally distinct organelles—the vegetative versus zygote cell wall—presents a likely scenario for the evolution of complex developmental gene regulatory networks.
C reactive protein in healthy term newborns during the first 48 hours of life

Background Early-onset neonatal sepsis (EOS) is a serious and potentially life-threatening disease in newborns. C reactive protein (CRP) is the most used laboratory biomarker for the detection of EOS. Little is known about normal reference values of CRP during the perinatal period as several factors are able to influence it. Objectives To identify an appropriate range of CRP values in healthy term newborns during the first 48 hours of life. Design CRP determination was performed in 859 term newborns at 12, 24 and 48 hours of life. Mode of delivery, maternal vaginal culture results, intrapartum antimicrobial prophylaxis (IAP) and other perinatal variables were recorded. Results CRP mean values were significantly higher at 48 hours (4.10 mg/L) than at both 24 (2.30 mg/L) and 12 hours of life (0.80 mg/L). CRP levels were affected by a number of perinatal proinflammatory variables. In particular, CRP mean values were significantly higher in babies born by vaginal delivery (3.80 mg/L) and emergency caesarean section (3.60 mg/L) than in babies born by elective caesarean section (2.10 mg/L). Completed course of IAP led to lower CRP mean values (2.90 mg/L) than IAP not completed (3.80 mg/L) or not performed (4.70 mg/L). Conclusions Postnatal age and mode of delivery significantly influence CRP values. Reliable reference values are crucial in order to obtain an adequate diagnostic accuracy.
Putative Adult Neurogenesis in Old World Parrots: The Congo African Grey Parrot (Psittacus erithacus) and Timneh Grey Parrot (Psittacus timneh)

In the current study, we examined for the first time, the potential for adult neurogenesis throughout the brain of the Congo African grey parrot (Psittacus erithacus) and Timneh grey parrot (Psittacus timneh) using immunohistochemistry for the endogenous markers proliferating cell nuclear antigen (PCNA), which labels proliferating cells, and doublecortin (DCX), which stains immature and migrating neurons. A similar distribution of PCNA and DCX immunoreactivity was found throughout the brain of the Congo African grey and Timneh grey parrots, but minor differences were also observed. In both species of parrots, PCNA and DCX immunoreactivity was observed in the olfactory bulbs, subventricular zone of the lateral wall of the lateral ventricle, telencephalic subdivisions of the pallium and subpallium, diencephalon, mesencephalon and the rhombencephalon. The olfactory bulb and telencephalic subdivisions exhibited a higher density of both PCNA and DCX immunoreactive cells than any other brain region. DCX immunoreactive staining was stronger in the telencephalon than in the subtelencephalic structures. There was evidence of proliferative hot spots in the dorsal and ventral poles of the lateral ventricle in the Congo African grey parrots at rostral levels, whereas only the dorsal accumulation of proliferating cells was observed in the Timneh grey parrot. In most pallial regions the density of PCNA and DCX stained cells increased from rostral to caudal levels with the densest staining in the nidopallium caudolaterale (NCL). The widespread distribution of PCNA and DCX in the brains of both parrot species suggest the importance of adult neurogenesis and neuronal plasticity during learning and adaptation to external environmental variations.
Influence of exogenous lactoferrin on the oxidant/antioxidant balance and molecular profile of hormone receptor-positive and -negative human breast cancer cells in vitro.

AIM To investigate the mechanisms of cytotoxic activity and pro-/antioxidant effect of lactoferrin on hormone receptor-positive and receptor-negative breast cancer cells in vitro. MATERIALS AND METHODS The study was performed on receptor-positive (MCF-7, T47D) and receptor-negative (MDA-MB-231, MDA-MB-468) human breast cancer cell lines. Immunocytochemical staining, flow cytometry, low-temperature electron paramagnetic resonance, and the Comet assay were used. RESULTS Upon treatment with lactoferrin, the increased levels of reactive oxygen species (ROS) (p < 0.05), NO generation rate by inducible NO-synthase (p < 0.05) and the level of "free" iron (p < 0.05) were observed. Moreover, the effects of lactoferrin were more pronounced in receptor-negative MDA-MB-231 and MDA-MB-468 cells. These changes resulted in increased expression of proapoptotic Bax protein (p < 0.05), reduced expression of the antiapoptotic Bcl-2 protein (p < 0.05) and level of not-oxidized mitochondrial cardiolipin (1.4-1.7-fold, p < 0.05). This, in turn, caused an increase in the percentage of apoptotic cells (by 14-24%, p < 0.05). Cytotoxic effects of lactoferrin were accompanied by an increase in the percentage of DNA in the comet tail and blocking cell cycle at G2/M phase, especially in receptor-negative cell lines. CONCLUSION The study showed that exogenous lactoferrin causes a violation of an antioxidant balance by increasing the level of ROS, "free" iron and NO generation rate, resalting in the blocking of cell cycle at G2/M-phase and apoptosis of malignant cells.
Residual stress distributions in laser and gas-metal-arc welded high-strength steel plates

S700 is a high-strength steel recently developed by Tata Steel. This paper describes the residual stress distributions in a multi-pass gas-metal-arc weld (GMAW), a single pass autogenous laser weld (ALW) and a multi-pass ultra-narrow gap laser weld (NGLW) in 13 mm thick high-strength (S700) steel plates, as measured by X-ray diffraction and the contour method. The relationships between microstructural variation and residual stress distributions were investigated. It was found that solid-sate phase transformations from austenite to ferrite, bainite and martensite changed both the magnitude and distribution of residual stresses in the three different welded specimens. The width of the regions sustaining tensile stress in each specimen decreased in the following order: GMAW > ALW > ultra-NGLW. This paper is part of a Themed Issue on Measurement, modelling and mitigation of residual stress.
Down on the upside: redemption, contamination, and agency in the lives of adult children of alcoholics

ABSTRACT We investigated differences in the nature and implications of Adult Children of Alcoholics (ACOAs; n = 53) and non-ACOAs’ (n = 80) narrative identities. Participants described six autobiographical narratives and completed measures of emotional functioning. Narratives were coded for redemptive (bad things turning good), contaminated (good things turning bad), and agentic (perceived control) imagery. ACOAs exhibited similar levels of redemptive and contaminated imagery, and lower levels of agency in their narratives, relative to non-ACOAs. In addition, themes of redemption, contamination, and agency corresponded divergently with emotional functioning. Among ACOAs, narrative redemption and agency were related to poorer emotional functioning whereas, among non-ACOAs, narrative contamination predicted poorer emotional functioning. These findings provide indication of the manner in which ACOAs story their lives. They also align with the emerging area of research noting that, among certain vulnerable populations, redemptive and agentic imagery serve as predictors of maladaptive functioning.
Treatment response in patients with idiopathic pulmonary arterial hypertension and a severely reduced diffusion capacity

Patients with idiopathic pulmonary arterial hypertension (IPAH) and a reduced diffusion capacity of the lung for carbon monoxide (DLCO) have a worse survival compared to IPAH patients with a preserved DLCO. Whether this poor survival can be explained by unresponsiveness to pulmonary hypertension (PH)-specific vasodilatory therapy is unknown. Therefore, the aim of this study was to evaluate the hemodynamic and cardiac response to PH-specific vasodilatory therapy in patients with IPAH and a reduced DLCO. Retrospectively, we studied treatment naïve hereditary and IPAH patients diagnosed between January 1990 and May 2015 at the VU University Medical Center. After exclusion of participants without available baseline DLCO measurement or right heart catheterization data and participants carrying a BMPR2 mutation, 166 participants could be included in this study. Subsequently, hemodynamics, cardiac function, exercise capacity, and oxygenation at baseline and after PH-specific vasodilatory therapy were compared between IPAH patients with a preserved DLCO (DLCO >62%), IPAH patients with a moderately reduced DLCO (DLCO 43–62%), and IPAH patients with a severely reduced DLCO (DLCO <43%). Baseline hemodynamics and right ventricular function were not different between groups. Baseline oxygenation was worse in patients with IPAH and a severely reduced DLCO. Hemodynamics and cardiac function improved in all groups after PH-specific vasodilatory therapy without worsening of oxygenation at rest or during exercise. Patients with IPAH and a severely reduced DLCO show a similar response to PH-specific vasodilatory therapy in terms of hemodynamics, cardiac function, and exercise capacity as patients with IPAH and a moderately reduced or preserved DLCO.
Characteristics of DO, organic matter, and ammonium profile for practical-scale DHS reactor under various organic load and temperature conditions

ABSTRACT Profile analysis of the down-flow hanging sponge (DHS) reactor was conducted under various temperature and organic load conditions to understand the organic removal and nitrification process for sewage treatment. Under high organic load conditions (3.21–7.89 kg-COD m−3 day−1), dissolved oxygen (DO) on the upper layer of the reactor was affected by organic matter concentration and water temperature, and sometimes reaches around zero. Almost half of the CODCr was removed by the first layer, which could be attributed to the adsorption of organic matter on sponge media. After the first layer, organic removal proceeded along the first-order reaction equation from the second to the fourth layers. The ammoniacal nitrogen removal ratio decreased under high organic matter concentration (above 100 mg L−1) and low DO (less than 1 mg L−1) condition. Ammoniacal nitrogen removal proceeded via a zero-order reaction equation along the reactor height. In addition, the profile results of DO, CODCr, and NH3-N were different in the horizontal direction. Thus, it is thought the concentration of these items and microbial activities were not in a uniform state even in the same sponge layer of the DHS reactor.
Identification of gene expression signatures across different types of neural stem cells with the Monte‐Carlo feature selection method

Adult neural stem cells (NSCs) are a group of multi‐potent, self‐renewing progenitor cells that contribute to the generation of new neurons and oligodendrocytes. Three subtypes of NSCs can be isolated based on the stages of the NSC lineage, including quiescent neural stem cells (qNSCs), activated neural stem cells (aNSCs) and neural progenitor cells (NPCs). Although it is widely accepted that these three groups of NSCs play different roles in the development of the nervous system, their molecular signatures are poorly understood. In this study, we applied the Monte‐Carlo Feature Selection (MCFS) method to identify the gene expression signatures, which can yield a Matthews correlation coefficient (MCC) value of 0.918 with a support vector machine evaluated by ten‐fold cross‐validation. In addition, some classification rules yielded by the MCFS program for distinguishing above three subtypes were reported. Our results not only demonstrate a high classification capacity and subtype‐specific gene expression patterns but also quantitatively reflect the pattern of the gene expression levels across the NSC lineage, providing insight into deciphering the molecular basis of NSC differentiation.
Integrative review of cervical cancer screening in Western Asian and Middle Eastern Arab countries

Population-based screening programs have resulted in minimizing mortality and morbidity from cervical cancer. The aim of this integrative review was to explore the factors influencing access of women from Western Asian and Middle Eastern Arab countries to cervical cancer screening. A systematic search for studies conducted in Arab countries in those regions, and published in English between January 2002 and January 2017, was undertaken. Thirteen papers were selected and subjected to quality appraisal. A three step analysis was used, which involved a summary of the evidence, analysis of both quantitative and qualitative data, and integration of the results in narrative form. Few population-based cervical cancer screening programs had been implemented in the relevant countries, with low knowledge of, and perceptions about, cervical screening among Arab women, the majority of whom are Muslim. Factors affecting the uptake of cervical cancer screening practices were the absence of organized, systematic programs, low screening knowledge among women, healthcare professionals' attitudes toward screening, pain and embarrassment, stigma, and sociocultural beliefs. Policy changes are urgently needed to promote population-based screening programs. Future research should address the promotion of culturally-sensitive strategies to enable better access of Arab Muslim women to cervical cancer screening.
Molecular Simulation Studies on the Binding Selectivity of Type-I Inhibitors in the Complexes with ROS1 versus ALK

ROS1 and ALK are promising targets of anticancer drugs for non-small-cell lung cancer. Since they have 49% amide acid sequence homology in the kinases domain and 77% identity at the ATP binding area, some ALK inhibitors also showed some significant responses for ROS1 in the clinical trial, such as the type-I binding inhibitor crizotinib and PF-06463922. As a newly therapeutic target, the selective ROS1 inhibitor is relatively rare. Moreover, the molecular basis for the selectivity of ROS1 versus ALK still remains unclear. In order to disclose the binding preference toward ROS1 over ALK and to aid the design of selective ROS1 inhibitors, the specific interactions and difference of conformational changes in the dual and selective ROS1/ALK inhibitors systems were investigated by molecular dynamics (MD) simulation and principle component analysis (PCA) in our work. Afterward, binding free energies (MM/GBSA) and binding free energies decomposition analysis indicated that the dominating effect of Van der Waals interaction drives the specific binding process of the type-I inhibitor, and residues of the P-loop and the DFG motif would play an important role in selectivity. On the basis of the modeling results, the new designed compound 14c was verified as a selective ROS1 inhibitor versus ALK, and SMU-B was a dual ROS1/ALK inhibitor by the kinase inhibitory study. These results are expected to facilitate the discovery and rational design of novel and specific ROS1 inhibitors.
Emotion, gender, and gender typical identity in autobiographical memory

ABSTRACT Gender differences in the emotional intensity and content of autobiographical memory (AM) are inconsistent across studies, and may be influenced as much by gender identity as by categorical gender. To explore this question, data were collected from 196 participants (age 18–40), split evenly between men and women. Participants narrated four memories, a neutral event, high point event, low point event, and self-defining memory, completed ratings of emotional intensity for each event, and completed four measures of gender typical identity. For self-reported emotional intensity, gender differences in AM were mediated by identification with stereotypical feminine gender norms. For narrative use of affect terms, both gender and gender typical identity predicted affective expression. The results confirm contextual models of gender identity (e.g., Diamond, 2012. The desire disorder in research on sexual orientation in women: Contributions of dynamical systems theory. Archives of Sexual Behavior, 41, 73–83) and underscore the dynamic interplay between gender and gender identity in the emotional expression of autobiographical memories.
GENERAL DESCRIPTION OF IDS INITIALLY INSTALLED AT ALBA

The new 3rd generation synchrotron radiation source ALBA built nearby Barcelona is planned to start operation in 2010 with several different insertion devices installed in the storage ring either from the beginning or within the first year of operation. The list of first insertion devices includes: 2 planar PPM SmCo in-vacuum undulators with the period of 21.6 mm; 2 Apple-II type PPM NdFeB undulators with the periods of 62.36 and 71.36 mm respectively; 1 superconducting planar wiggler with the period of 30 mm and a maximum field of 2.1 T, and a 1 conventional wiggler with the period of 80.0 mm and a maximum field of 1.74 T. The emitted light of these IDs covers wide spectral range extending from hard Xrays to UV. Pre-design of the IDs was done by ALBA, but manufacturing has been outsourced. Production is now finished and they have been tested with magnetic measurements. The paper will present the final as build magnetic designs as well as the main results of magnetic measurements performed on the manufactured devices.
Species-Specific 5 mC and 5 hmC Genomic Landscapes Indicate Epigenetic Contribution to Human Brain Evolution

Human evolution from non-human primates has seen substantial change in the central nervous system, with the molecular mechanisms underlying human brain evolution remaining largely unknown. Methylation of cytosine at the fifth carbon (5-methylcytosine; 5 mC) is an essential epigenetic mark linked to neurodevelopment, as well as neurological disease. The emergence of another modified form of cytosine (5-hydroxymethylcytosine; 5 hmC) that is enriched in the brain further substantiates a role for these epigenetic marks in neurodevelopment, yet little is known about the evolutionary importance of these marks in brain development. Here, human and monkey brain tissue were profiled, identifying 5,516 and 4,070 loci that were differentially methylated and hydroxymethylated, respectively, between the species. Annotation of these loci to the human genome revealed genes critical for the development of the nervous system and that are associated with intelligence and higher cognitive functioning, such as RELN and GNAS. Moreover, ontological analyses of these differentially methylated and hydroxymethylated genes revealed a significant enrichment of neuronal/immunological–related processes, including neurogenesis and axon development. Finally, the sequences flanking the differentially methylated/hydroxymethylated loci contained a significant enrichment of binding sites for neurodevelopmentally important transcription factors (e.g., OTX1 and PITX1), suggesting that DNA methylation may regulate gene expression by mediating transcription factor binding on these transcripts. Together, these data support dynamic species-specific epigenetic contributions in the evolution and development of the human brain from non-human primates.
International Journal of Women's Health Dovepress Hematoma and Abscess Formation Caused by Mycoplasma Hominis following Cesarean Section

Mycoplasma species cannot be identified by routine bacteriological culture methods and are resistant to common antimicrobial agents. Mycoplasma hominis usually colonizes the lower urogenital tract and causes pyelonephritis, pelvic inflammatory disease, chorioamnionitis, rupture of fetal membranes, preterm labor, postpartum fever, postabortal fever, and neonatal infection. This organism is highly prevalent in cervicovaginal cultures of sexually active women. M. hominis, M. genitalis, Ureaplasma urealyticum, and U. parvum may invade and infect placental and fetal tissues, leading to adverse pregnancy outcomes. M. hominis occasionally causes nongenitourinary infection of the blood, wounds, central nervous system, joints, or respiratory tract. We present a case of a 27-year-old woman who developed abdominal wound hematoma and abscess after cesarean section. The wound was drained, but her high fever persisted, in spite of antibiotic treatment using flomoxef sodium and imipenem⋅cilastatin sodium. Because the exudate exhibited M. hominis growth in an anaerobic environment, we administered the quinolone ciprofloxacin. This therapy resolved her fever, and her white blood cell count and C-reactive protein level diminished to the normal ranges. To our knowledge, there are four published articles regarding the isolation of M. hominis from postcesarean incisions. Based on the current study and the literature, infection by this pathogen may cause hematoma formation with or without abscess after cesarean section or in immunosuppressed postoperative patients. In such cases, physicians may need to suspect Mycoplasma infection and initiate appropriate antibacterial treatment as soon as possible in order to avoid persistent fever.
A Hybrid Word-Character Model for Abstractive Summarization

Abstractive summarization is the popular research topic nowadays. Due to the difference in language property, Chinese summarization also gains lots of attention. Most of studies use character-based representation instead of word-based to keep out the error introduced by word segmentation and OOV problem. However, we believe that word-based representation can capture the semantics of the articles more accurately. We proposed a hybrid word-character model preserves the advantage of both word-based and character-based representations. Our method also enables us to use larger word vocabulary size than anyone else. We call this new method HWC (Hybrid Word-Character). We conduct the experiments on LCSTS Chinese summarization dataset, and out-perform the current state-of-the-art by at least 8 ROUGE points.