Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypoxia and sFlt-1 in preeclampsia: the "chicken-and-egg" question.

Preeclampsia is a disorder of pregnancy that is usually characterized by the appearance of proteinuria and hypertension during the third trimester of pregnancy (1). It is a common disorder, occurring in 5% of all pregnancies, and often requires premature delivery of the baby. Occasionally, preeclampsia may lead to seizures and multiorgan dysfunction in the mother with severe morbidity and even mortality. Preeclampsia occurs only in the presence of placenta and remits dramatically postpartum, after the placenta has been delivered (2). The placentae of preeclamptic women appear abnormal, with evidence of underperfusion and ischemia. The initiating event in preeclampsia has been postulated to be reduced uteroplacental perfusion as a result of abnormal cytotrophoblast invasion of spiral arterioles (3, 4). Overwhelming evidence points to endothelial dysfunction as the central mechanism in the pathogenesis of the maternal syndrome in preeclampsia (5). This has led to a hypothesis put forth by Roberts et al. (6, 7) that the ischemic placenta secretes soluble factors into the maternal vasculature. This, in turn, induces endothelial dysfunction and the clinical features of preeclampsia. Several groups including our laboratory have recently presented evidence that excess secretion of a naturally occurring antiangiogenic molecule of placental origin referred to as soluble fms-like tyrosine kinase-1 (sFlt-1, also referred to as sVEGFR-1) may cause the maternal syndrome (8–14). sFlt-1 acts by antagonizing proangiogenic molecules such as vascular endothelial growth factor (VEGF) and placental growth factor (PlGF) (15). The excess sFlt-1 production in preeclampsia has been hypothesized to be secondary to placental ischemia/hypoxia (12). However, it was unclear how hypoxia would affect the net angiogenic balance in the placenta because VEGF, a proangiogenic molecule, is also up-regulated by hypoxia (16). A report in this issue of Endocrinology [Nagamatsu et al. (17)] provides new evidence that effects of hypoxia are cell type specific and that in placental cytotrophoblasts (in contrast to endothelial cells), hypoxia induces an excess production of sFlt-1. This leads to VEGF deficiency and, consequently, an antiangiogenic state.
Aberrant Rac pathway signalling in glioblastoma

ABSTRACT Glioblastoma is an aggressive and incurable form of brain cancer. Both mutation analysis in human glioblastoma and mouse modelling studies have shown that aberrant activation of the PI 3-kinase pathway is a central driver of glioblastoma malignancy. The small GTPase Rac is activated downstream of this pathway, mediating a subset of the effects of aberrant PI 3-kinase pathway activation. Here I discuss the current state of our knowledge on Rac activation mechanisms in glioblastoma. Current knowledge on roles for specific PI 3-kinase pathway responsive Rac guanine nucleotide exchange factors in glioblastoma is reviewed. Rac is best known for its role in promoting cell motility and invasion, but there is also evidence for roles in multiple other cellular processes with cancer relevance, including proliferation, differentiation, apoptosis, DNA damage responses, metabolism, angiogenesis and immunosuppression. I review what is known about the role of Rac in these processes in glioblastoma. Finally, I assess possible strategies to inhibit this pathway in glioblastoma through either direct inhibition of Rac or inhibition of upstream activators or downstream mediators of Rac signalling.
Revealing the Amylase Interactome in Whole Saliva Using Proteomic Approaches

Understanding proteins present in saliva and their function when isolated is not enough to describe their real role in the mouth. Due to protein-protein interactions, structural changes may occur in macromolecules leading to functional modulation or modification. Besides amylase's function in carbohydrate breakdown, amylase can delay proteolytic degradation of protein partners (e.g., histatin 1) when complexed. Due to its biochemical characteristics and high abundance in saliva, amylase probably interacts with several proteins acting as a biological carrier. This study focused on identifying interactions between amylase and other proteins found in whole saliva (WS) using proteomic approaches. Affinity chromatography was used, followed by gel electrophoresis methods, sodium dodecyl sulfate and native, tryptic in-solution and in-gel digestion, and mass spectrometry. We identified 66 proteins that interact with amylase in WS. Characterization of the identified proteins suggests that acidic (pI < 6.8) and low molecular weight (MW < 56 kDa) proteins have preference during amylase complex formation. Most of the identified proteins present biological functions related to host protection. A new protein-amylase network was constructed using the STRING database. Further studies are necessary to investigate individualities of the identified amylase interactors. These observations open avenues for more comprehensive studies on not yet fully characterized biological function of amylase.
TiCoNE 2: A Composite Clustering Model for Robust Cluster Analyses on Noisy Data.

Identifying groups of similar objects using clustering approaches is one of the most frequently employed first steps in exploratory biomedical data analysis. Many clustering methods have been developed that pursue different strategies to identify the optimal clustering for a data set. We previously published TiCoNE, an interactive clustering approach coupled with de-novo network enrichment of identified clusters. However, in this first version time-series and network analysis remained two separate steps in that only time-series data was clustered, and identified clusters mapped to and enriched within a network in a second separate step. In this work, we present TiCoNE 2: An extension that can now seamlessly incorporate multiple data types within its composite clustering model. Systematic evaluation on 50 random data sets, as well as on 2,400 data sets containing enriched cluster structure and varying levels of noise, shows that our approach is able to successfully recover cluster patterns embedded in random data and that it is more robust towards noise than non-composite models using only one data type, when applied to two data types simultaneously. Herein, each data set was clustered using five different similarity functions into k=10/30 clusters, resulting to ~5,000 clusterings in total. We evaluated the quality of each derived clustering with the Jaccard index and an internal validity score. We used TiCoNE to calculate empirical p-values for all generated clusters with different permutation functions, resulting in ~80,000 cluster p-values. We show, that derived p-values can be used to reliably distinguish between foreground and background clusters. TiCoNE 2 allows researchers to seamlessly analyze time-series data together with biological interaction networks in an intuitive way and thereby provides more robust results than single data type cluster analyses.
Upper Lid Blepharoplasty Without Cutting the Orbicularis Muscle

We have compared the aesthetic outcomes of upper blepharoplasty with or without resection of the preseptal orbicularis oculi muscle. In addition we evaluated MRI to visualize the differences in the upper eyelids before and after surgery. An interventional randomized double-blind left right study was conducted in 10 patients with upper eyelid dermatochalazis. One side was randomly chosen for incision of the preseptal orbicularis oculi muscle and direct coagulation or resection of fat pockets. The orbicularis oculi muscle of the contralateral side was not incised. Only a soft coagulation was performed on the muscle to induce a septal contraction and push the orbital fat back. All interventions were performed with an Ellman Dual frequency high frequency low temperature unit. Digital photos were taken before and after surgery and patients were asked to fill in a questionnaire to evaluate the surgery itself as well as the aesthetic outcome. In an attempt to objectify these findings, NMR imaging of the orbits was performed before and 6 weeks after surgery. Symptoms scoring was similar in both groups. At 6 weeks post-operation, no significant differences were observed between left and right eye. In conclusion, patients with dermatochalazis but without prominent fat prolapse in the upper eyelid, did not exhibit significant differences after cutting or not the orbicularis muscle to excise orbital fat. Even in cases with moderate fat prolapse, the fat can be pushed back by soft coagulation of the orbicularis and underlying orbital septum. When the preseptal orbicularis oculi muscle is preserved, the risk of hematoma and orbital cellulitis can be limited.
Living Shorelines: Coastal Resilience with a Blue Carbon Benefit

Living shorelines are a type of estuarine shoreline erosion control that incorporates native vegetation and preserves native habitats. Because they provide the ecosystem services associated with natural coastal wetlands while also increasing shoreline resilience, living shorelines are part of the natural and hybrid infrastructure approach to coastal resiliency. Marshes created as living shorelines are typically narrow (< 30 m) fringing marshes with sandy substrates that are well flushed by tides. These characteristics distinguish living shorelines from the larger meadow marshes in which most of the current knowledge about created marshes was developed. The value of living shorelines for providing both erosion control and habitat for estuarine organisms has been documented but their capacity for carbon sequestration has not. We measured carbon sequestration rates in living shorelines and sandy transplanted Spartina alterniflora marshes in the Newport River Estuary, North Carolina. The marshes sampled here range in age from 12 to 38 years and represent a continuum of soil development. Carbon sequestration rates ranged from 58 to 283 g C m-2 yr-1 and decreased with marsh age. The pattern of lower sequestration rates in older marshes is hypothesized to be the result of a relative enrichment of labile organic matter in younger sites and illustrates the importance of choosing mature marshes for determination of long-term carbon sequestration potential. The data presented here are within the range of published carbon sequestration rates for S. alterniflora marshes and suggest that wide-scale use of the living shoreline approach to shoreline management may come with a substantial carbon benefit.
The Role of Epstein–Barr Virus in Cervical Cancer: A Brief Update

Epstein–Barr virus (EBV) belongs to the group of gamma-herpes viruses and was the first recognized human oncovirus. EBV is responsible for infectious mononucleosis and multiple lymphoid and epithelial malignancies including B-cell lymphomas (Burkitt lymphoma, Hodgkin lymphoma, and post-transplant lymphoproliferative disorder), various T-cell/NK lymphoproliferative disorders, nasopharyngeal carcinoma, and gastric carcinoma, respectively. In addition, the presence of EBV has been documented in other cancers including breast, prostate, oral, and salivary gland carcinomas. The presence and role of EBV in cervical cancer and its precursor lesions (CIN) have also been described, but the results from the literature are inconsistent, and the causal role of EBV in cervical cancer pathogenesis has not been established yet. In the present review, we briefly surveyed and critically appraised the current literature on EBV in cervical cancer and its variants (lymphoepithelioma-like carcinoma) as well as its precursor lesions (CIN). In addition, we discussed the possible interactions between EBV and human papilloma virus as well as between EBV and immune checkpoint regulators (PD-L1). Though further studies are needed, the available data suggest a possible causal relationship between EBV and cervical cancer pathogenesis.
Soft Marginal TransE for Scholarly Knowledge Graph Completion

Knowledge graphs (KGs), i.e. representation of information as a semantic graph, provide a significant test bed for many tasks including question answering, recommendation, and link prediction. Various amount of scholarly metadata have been made vailable as knowledge graphs from the diversity of data providers and agents. However, these high-quantities of data remain far from quality criteria in terms of completeness while growing at a rapid pace. Most of the attempts in completing such KGs are following traditional data digitization, harvesting and collaborative curation approaches. Whereas, advanced AI-related approaches such as embedding models - specifically designed for such tasks - are usually evaluated for standard benchmarks such as Freebase and Wordnet. The tailored nature of such datasets prevents those approaches to shed the lights on more accurate discoveries. Application of such models on domain-specific KGs takes advantage of enriched meta-data and provides accurate results where the underlying domain can enormously benefit. In this work, the TransE embedding model is reconciled for a specific link prediction task on scholarly metadata. The results show a significant shift in the accuracy and performance evaluation of the model on a dataset with scholarly metadata. The newly proposed version of TransE obtains 99.9% for link prediction task while original TransE gets 95%. In terms of accuracy and Hit@10, TransE outperforms other embedding models such as ComplEx, TransH and TransR experimented over scholarly knowledge graphs
An energy-based background modelling algorithm for motion detection

Detecting moving objects is very important in many application contexts such as people detection, visual surveillance, automatic generation of video effects, and so on. The first and fundamental step of all motion detection algorithms is the background modeling. The goal of the methodology here proposed is to create a background model substantially independent from each hypothesis about the training phase, as the presence of moving persons, moving background objects, and changing (sudden or gradual) light conditions. We propose an unsupervised approach that combines the results of temporal analysis of pixel intensity with a sliding window procedure to preserve the model from the presence of foreground moving objects during the building phase. Moreover, a multilayered approach has been implemented to handle small movements in background objects. The algorithm has been tested in many different contexts, such as a soccer stadium, a parking area, a street, a beach. Finally, it has been tested even on the CAVIAR 2005 dataset.
Autophagy is increased in cryptorchid testis resulting in abnormal spermatozoa

Autophagy is involved in spermatogenesis by regulating germ cell maturation. This catabolic process increases with hyperthermic conditions to prevent the accumulation of damaged organelles. Cryptorchidism is associated with impairment of germ cell maturation revealed by the presence of immature forms of sperm cells in ejaculates. The aim of the present study was to evaluate the status of autophagy in sperm cells from cryptorchid patients. Semen samples of cryptorchid patients and normozoospermic controls were analyzed by immunocytochemistry and electron microscopy. Autophagy proteins, autophagy-related protein 9 (ATG9) and microtubule-associated protein, 1A/1B-light chain 3 (LC3) were localized by immunocytochemistry on the acrosome and on the equatorial segment of sperm cells. LC3 was also detected in the midpiece of cryptorchid sperm tail. Autophagy substrate p62 protein was present in the acrosome and in the postequatorial segment of sperm in control samples, but not in the cryptorchid ones. Transmission electron microscopy revealed double-membrane-limited autophagosomes in postequatorial part of spermatozoa head and midpiece in cryptorchid samples. Partly degraded mitochondria were frequently discerned in autophagic vacuoles. In conclusion, autophagy is increased in sperm cells from patients with cryptorchid history comparatively to control. Our work provides insights into the role of autophagy in the maturation and survival of human male gametes in pathological conditions. Thus, regulating autophagy could represent a potential way to improve sperm quality in cryptorchid men.
Practical whole-system provenance capture

Data provenance describes how data came to be in its present form. It includes data sources and the transformations that have been applied to them. Data provenance has many uses, from forensics and security to aiding the reproducibility of scientific experiments. We present CamFlow, a whole-system provenance capture mechanism that integrates easily into a PaaS offering. While there have been several prior whole-system provenance systems that captured a comprehensive, systemic and ubiquitous record of a system's behavior, none have been widely adopted. They either A) impose too much overhead, B) are designed for long-outdated kernel releases and are hard to port to current systems, C) generate too much data, or D) are designed for a single system. CamFlow addresses these shortcoming by: 1) leveraging the latest kernel design advances to achieve efficiency; 2) using a self-contained, easily maintainable implementation relying on a Linux Security Module, NetFilter, and other existing kernel facilities; 3) providing a mechanism to tailor the captured provenance data to the needs of the application; and 4) making it easy to integrate provenance across distributed systems. The provenance we capture is streamed and consumed by tenant-built auditor applications. We illustrate the usability of our implementation by describing three such applications: demonstrating compliance with data regulations; performing fault/intrusion detection; and implementing data loss prevention. We also show how CamFlow can be leveraged to capture meaningful provenance without modifying existing applications.
Learning Multimodal Neural Network with Ranking Examples

To support cross-modal information retrieval, cross-modal learning to rank approaches utilize ranking examples (e.g., an example may be a text query and its corresponding ranked images) to learn appropriate ranking (similarity) function. However, the fact that each modality is represented with intrinsically different low-level features hinders these approaches from better reducing the heterogeneity-gap between the modalities and thus giving satisfactory retrieval results. In this paper, we consider learning with neural networks, from the perspective of optimizing the listwise ranking loss of the cross-modal ranking examples. The proposed model, named Cross-Modal Ranking Neural Network (CMRNN), benefits from the advance of both neural networks on learning high-level semantics and learning to rank techniques on learning ranking function, such that the learned cross-modal ranking function is implicitly embedded in the learned high-level representation for data objects with different modalities (e.g., text and imagery) to perform cross-modal retrieval directly. We compare CMRNN to existing state-of-the-art cross-modal ranking methods on two datasets and show that it achieves a better performance.
Nanowire photodetectors based on wurtzite semiconductor heterostructures

Using nanowires for photodetection constitutes an opportunity to enhance the absorption efficiency while reducing the electrical cross-section of the device. Nanowires present interesting features like compatibility with silicon substrates, which offers the possibility of integrating detector and readout circuitry and facilitates their transfer to flexible substrates. The incorporation of heterostructures in nanowire photodetectors opens interesting prospects for application and performance improvement. Within a nanowire, it is possible to implement axial and radial (core-shell) heterostructures, and these two types can be combined to obtain the three-dimensional carrier confinement (dot-in-a-wire) which is required for the development of quantum photodetectors. If the nanowires present wurtzite crystallographic structure, the presence of heterointerfaces can induce internal electric fields due to the difference of polarization between the constituents. Such polarization-induced internal electric fields, like those induced by heterojunctions or type-II heterostructures, can be ingeneered to favor the separation of the photogenerated electrons and holes. This paper provides a general review of latest progresses in nanowire photodetectors, including single nanowires and heterostructured nanowires.
Spermatozoa Expression of piR-31704, piR-39888, and piR-40349 and Their Correlation to Sperm Concentration and Fertilization Rate After ICSI

Objective: To investigate the relationship between spermatozoa PIWI-interacting RNAs (piRNAs) levels and semen parameters and to evaluate the role of expression of piRNAs on fertilization and embryo development after intracytoplasmic sperm injection (ICSI) treatment. Methods: One hundred and eighty-six patients with idiopathic male infertility who had undergone first ICSI cycles were enrolled in our study. The levels of piRNAs in spermatozoa were measured by real-time polymerase chain reaction. Semen parameters, including sperm concentration, motility, and morphology, were evaluated. The rates of fertilization, early cleavage, and day 3 good-quality embryo were calculated to assess embryo development potential. Result: Spermatozoa levels of piR-31704 and piR-39888 were decreased in male factor infertility group as compared with control group (for piR-31704, P = .027 and for piR-39888, P = .041, respectively). And these 2 piRNAs were expressed at higher levels in patients with normal sperm concentration compared with subnormal sperm concentration group (for piR-31704, P = .042; for piR-39888, P = .047, respectively), while there were no correlation between the 3 piRNAs expression levels in spermatozoa and the rates of sperm progressive motility and normal sperm morphology. There were significant increases in the levels of all 3 piRNAs in spermatozoa from the group with higher 2PN rates (for piR-31704, P = .002; for piR-39888, P < .001; for piR-40349, P < .001; respectively), but there was no correlation between spermatozoa levels of these 3 piRNAs and the rates of embryo early cleavage, day 3 good-quality embryos and pregnancy. Conclusion: Spermatozoa piRNA levels correlate with sperm concentration and fertilization rate after ICSI. Paternal piRNAs may play a role in fertilization process.