bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive models for secondary epilepsy in patients with acute ischemic stroke within one year
Authors: Liu Jinxin , He Haoyue , Wang Yanglingxi , Du Jun , Liang Kaixin , Xue Jun , Liang Yidan , Chen Peng , Tian Shanshan , Deng Yongbing 
Published: November 2024

Background:Post-stroke epilepsy (PSE) is a critical complication that worsens both prognosis and quality of life in patients with ischemic stroke. An interpretable machine learning model was developed to predict PSE using medical records from four hospitals in Chongqing.Methods:Medical records, imaging reports, and laboratory test results from 21,459 ischemic stroke patients were collected and analyzed. Univariable and multivariable statistical analyses identified key predictive factors. The dataset was split into a 70% training set and a 30% testing set. To address the class imbalance, the Synthetic Minority Oversampling Technique combined with Edited Nearest Neighbors was employed. Nine widely used machine learning algorithms were evaluated using relevant prediction metrics, with SHAP (SHapley Additive exPlanations) used to interpret the model and assess the contributions of different features.Results:Regression analyses revealed that complications such as hydrocephalus, cerebral hernia, and deep vein thrombosis, as well as specific brain regions (frontal, parietal, and temporal lobes), significantly contributed to PSE. Factors such as age, gender, NIH Stroke Scale (NIHSS) scores, and laboratory results like WBC count and D-dimer levels were associated with increased PSE risk. Tree-based methods like Random Forest, XGBoost, and LightGBM showed strong predictive performance, achieving an AUC of 0.99.Conclusions:The model accurately predicts PSE risk, with tree-based models demonstrating superior performance. NIHSS score, WBC count, and D-dimer were identified as the most crucial predictors.Funding:The research is funded by Central University basic research young teachers and students research ability promotion sub-projec t(2023CDJYGRH-ZD06), and by Emergency Medicine Chongqing Key Laboratory Talent Innovation and development joint fund project (2024RCCX10).
Cultivating a Sustainable Future: Modern Agriculture in Peri-Urban Food Security
Authors: Mukhlis Imam , Suwanan Ahmad Fawaiq , Priambodo Magistyo Purboyo , Munir Syahrul , Cahayati Nila 
Published: November 2024

This study aims to explore the phenomenon of food security and identify the contribution of modern agriculture in overcoming food security problems in the peri-urban area of East Java. In recent decades, the development of Jongbiru areas has undergone a rapid transformation into an urban area where industrial development is relatively rapid and large. This research design is carried out through the Community pilot project development model scheme and FGD with stakeholders in the peri-urban area of East Java, Indonesia. Through the PRA-pilot project approach, this research found challenges faced by the community. Knowledge, skills regarding modern agricultural (particularly in hydroponic), accessibility about their economic viability being the major challenges to faced. The results show there are lot of postive responds from the pilot project. Participants eager to implement the material knowledge by themself at their own home. Further, this PRA have potential for village economic development and support the achievement of the SDGs, such as poverty alleviation, food security, and the promotion of sustainable agricultural innovation. The study also emphasizes the importance of policy and infrastructure support to ensure the initiative's sustainability, which aligns with the literature highlighting the importance of millennial involvement in agricultural innovation.
A Review on Advanced Preservation Techniques for Post-harvest Quality Maintenance of Fruits and Vegetables
Authors: Maurya Hareesh Kumar , Lata Rubee , Mitra Diksha Sangh , Sundar Shyam , Yadav G. C. 
Published: November 2024

Fruits and vegetables preservation is critical for reducing post-harvest losses, increasing shelf life, and ensuring year-round availability of seasonal goods. It approach is meant to preserve the nutritional value, taste, texture, and color of fresh food while preventing spoiling caused by microbes, enzymes, and environmental influences. There are three types of preservation methods: physical, chemical, and biological. Refrigeration, freezing, and drying are examples of physical preservation processes, as are heat treatments like pasteurization and canning. Refrigeration reduces microbial growth and enzymatic activity, whereas freezing stops both, allowing fruits and vegetables to be stored for longer periods. Drying procedures include sun-drying, dehydration, vacuum drying, and freeze-drying, all of which remove moisture and restrict microbial activity. Canning is the method of destroying microorganisms with heat and putting them in an airtight container to prevent contamination. Chemical preservation methods include sulphur dioxide, sodium benzoate, and citric acid. Sugar, salt, acids, and spices are food additives used to preserve fruits and vegetables. In Fermentation, microorganisms such as bacteria and yeast convert sugars into acids or alcohol, producing an environment that prevents spoilage organisms from growing. Finally, conclusion preserving fruits and vegetables is an important part of food security and quality management. A combination of traditional and modern technologies, suited to the individual demands of different types of produce, is critical for reducing waste and providing a consistent supply of nutritious foods year-round.
Yeasts
Authors: Lachance Marc‐André , Walker Graeme M 
Published: October 2018

Abstract

Yeasts are a group of eukaryotic microfungi with a well‐defined cell wall whose growth is either entirely unicellular or a combination of hyphal and unicellular reproduction. The approximately 1500 known yeast species belong to two distinct fungal phyla, the Ascomycota and the Basidiomycota. Within each of these phyla, yeasts can be found in several subphyla or classes, reflecting the enormous diversity of their evolutionary origins and biochemical properties. In nature, yeasts are found mainly in association with plants or animals but are also present in soil and aquatic environments. Yeasts grow rapidly and have simple nutritional requirements, for whieh reason they have been used as model systems in biochemistry, genetics and molecular biology. They were the first microorganisms to be domesticated for the production of beer, bread or wine, and they continue to be used for the benefit of humanity in the production of many important health care and industrial commodities, including recombinant proteins, biopharmaceuticals, biocontrol agents and biofuels. The best‐known yeast is the species
Saccharomyces cerevisiae
, which may be regarded as the world's foremost industrial microbe.

Key Concepts

Yeasts share in common a primarily unicellular mode of reproduction.

Yeasts are phylogenetically diverse, being classified in several classes of two fungal phyla.

The concept of yeast is rooted in history and does not always follow logical biological lines.

Yeasts have a rigid cell wall primarily made up of β‐(1–3)‐glucan.

Sexual reproduction in yeasts involves the formation of internally formed ascospores or externally formed basidiospores.

Current yeast classification is based on phylogenetic relationships inferred by gene sequencing.

Yeasts grow in nature primarily in association with the plant–insect interface or with warm‐blooded animals, but also occur in soil and aquatic habitats.

Yeasts serve as important industrial model systems in research.

Yeasts are of great importance in biotechnology. The main products are alcohol, yeast biomass and recombinant proteins.
Saccharomyces cerevisiae
is the premier industrial microorganism.

A few yeast species cause infections in humans and other animals, but most yeasts act in an opportunistic manner, in individuals that are immunocompromised.
RNA
Polymerase
II
and Associated Transcription Factors
Authors: Karmakar Saswati , Ponnusamy Moorthy P , Bhaumik Sukesh R , Batra Surinder K 
Published: October 2018

Abstract

Transcription of protein‐coding genes to messenger ribonucleic acid (mRNA) is a tightly regulated multistep process involving the spatial and temporal recruitment of numerous proteins and protein complexes to the genes. The three main steps of the process are transcription initiation with the formation of the transcription preinitiation complex, elongation, and termination. All these steps involve a protein complex known as RNA polymerase II that interacts with many factors during initiation, elongation and termination to regulate transcription, chromatin structure, mRNA processing and export, and associated deoxyribonucleic acid repair. This article focuses on RNA polymerase II and associated factors during transcriptional initiation and early stage of transcriptional elongation. RNA polymerase II
C
‐terminal domain phosphorylation and its functions in transcription cycle are also described. Further, a brief description of RNA polymerase II holoenzyme complexes is included here.

Key Concepts

Transcription is a multistep process consisting of initiation, elongation and termination for RNA (ribonucleic acid) synthesis.

RNA polymerase II (RNAPII) is a key enzyme/factor in transcription of the protein‐coding genes to messenger RNA (mRNA).

Transcriptional initiation of the protein‐coding genes occurs at the promoter via formation of the preinitiation complex (PIC), an assembly of general transcription factors (GTFs) and RNAPII.

The core elements of the promoter (or core promoter) are involved in formation of PIC for transcriptional initiation.

PIC formation at the core promoter is regulated by gene‐specific factors such as enhancers and repressors.

Shortly after transcriptional initiation, RNAPII pauses at the promoter‐proximal site, and subsequently, it is released following phosphorylation for productive transcriptional elongation.
Viral Infections of the Central Nervous System
Authors: Chávez‐Pavoni Juliana H 
Published: October 2018

Abstract

Viral infections of the central nervous system (CNS) represent a significant burden to human health worldwide. Many viruses are able to cause neurologic disease such as herpes virus (HSV), varicella zoster virus (VZV), cytomegalovirus (CMV), Epstein–Barr virus (EBV), human enterovirus (HEV), rabies virus (RV) and arboviruses. Viral access to CNS is defined by two main routes, the haematogenous or peripheral nerve pathway. During a viral infection in the CNS, inflammation and damage can arise in distinct anatomical regions, such as the meninges, brain and spinal cord or even simultaneously in multiple regions (meningoencephalitis, encephalomyelitis). Diagnosis of these infections is crucial in order to establish adequate management and prevent sequelae.

Key Concepts

Viral infection of the central nervous system may present different viruses as causative agents.

Central nervous system is protected by a highly complex barrier system represented by blood–brain and blood–cerebrospinal fluid barriers.

Neurotropic viruses dribble blood–brain barriers through different ways.

Once established in the central nervous system, viral infection results in inflammation and damage, which can affect distinct anatomical areas.

Viral meningitis or aseptic meningitis includes inflammation restricted to the leptomeninges, the tissue which covers and protect the brain.

Viral encephalitis refers to inflammation and damage comprising the brain parenchyma.

Viral myelitis is defined by the inflammation that affects exclusively the spinal cord.

Some viruses cause extended neurologic involvement which result in meningoencephalitis or encephalomyelitis.

Diagnosis of infections of central nervous system is based on clinical picture, laboratorial findings and imaging techniques.

Adequate management of viral infections of central nervous system are crucial in order to prevent sequelae.
From Foe to Friend: Therapeutic and Commercial Applications of Engineered Viruses
Authors: DeHart Jason L , Kamrud Kurt I 
Published: October 2018

AbstractViruses were first discovered over 120 years ago as filterable pathogens. Since then, our understanding of virus biology has moved from filterable agents capable of causing disease to an in‐depth mechanistic understanding of both viral replication and the diseases they cause. They have served as road maps and tools leading to the discovery of RNA splicing, oncogenes and tumour suppressors as well as unlocked our understanding of basic cell biology, tumourigenesis and the complexities of the immune system. Although there is still much to learn, the information we have gleaned over the past century highlights the efficiency, adaptability and power contained within these small packages. However, until recently, the techniques used to manipulate and engineer viral genomes were limited and cumbersome. They frequently relied on a combination of traditional molecular biology and virology techniques and could take weeks to months to introduce single mutations. Recent advances in molecular biology along with tools to synthesise DNA have reduced the time to engineer viral genomes from months to days, and in some cases hours. As a result, engineered and synthetic viruses have begun to move from mere pathogens to powerful machines that can be applied in a wide array of therapeutic and commercial applications.Key ConceptsAdvances in DNA synthesis and molecular biology are facilitating our ability to engineer and synthesise viral genomes.Modern molecular biology can improve the safety of virus‐based therapeutics.Synthetic virology provides an opportunity to improve and accelerate the existing vaccine development.Synthetic and engineered viruses can be used in a wide range of therapeutic and nontherapeutic applications.Synthetic viruses can be used as tools to understand both viral replication and cell biology.
Dual‐Specificity
R
as/
R
ap
GTPase
Activating Proteins
Authors: Sot Begoña 
Published: October 2018

Abstract

The small GTP‐binding proteins Ras and Rap regulate important cellular events switching between an activated GTP‐bound form and an inactivated GDP‐bound state. Guanine exchange factors (GEFs) control the GDP to GTP‐bound cycle, while the conversion, through hydrolysis, of GTP to GDP is catalysed by GTPase‐activating proteins (GAPs). The GAPs complete Ras and Rap catalytic site for efficient GTP hydrolysis. Although Ras and Rap are highly homologous, they possess different residues in the catalytic site. In consequence, Ras and Rap GTPase‐activating proteins (RasGAPs and RapGAPs) are structurally unrelated and use different mechanisms. Surprisingly, there are several RasGAPs with dual Ras/Rap specificity: SynGAP; GAP1 family members GAP1
IP4BP
, Rasal and Capri; and Plexins. This characteristic was an intriguing issue for years, but today structural and biochemical studies have enlightened the overall general mechanism of these dual GAPs.

Key Concepts

Small GTP‐binding proteins Rap and Ras control different cellular signalling switching between inactive GDP and active GTP‐bound states.

Ras and Rap GTPase‐activating proteins (RasGAPs and RapGAPs) inactivate their downstream signalling catalysing the GTP hydrolysis, using RasGAP and RapGAP domains.

RasGAPs–Ras‐GTP interaction positions Ras Gln61, situated in switch II loop, for nucleophilic attack, while the GAP contributes an Arg (arginine finger) to neutralise unfavourable negative charges of the reaction intermediate.

Rap has a Thr in position 61, and RapGAPs catalyse GTP hydrolysis, contributing an Asn (Asn thumb) for nucleophilic attack.

There are five RasGAPs with dual Rap/Ras specificity: SynGAP, Rasal, GAP1
IP4BP
, Capri and Plexin.

Dual GAPs need extra‐GAP domains to act as RapGAPs.

Dual GAPs promote a specific orientation of Rap switch II, locating Gln63 as the catalytic residue.

Plexin‐Rap X‐ray structure showed that residues of GAP domain and an extra‐GAP motif (juxtamembrane segment) are responsible for Gln63 correct orientation.

SynGAP, Rasal, GAP1
IP4BP
, Plexin and Capri do not share the same residues, and thus they still need to be found.
Cervical skin denervation associates with alpha‐synuclein aggregates in Parkinson disease
Authors: Melli Giorgia , Vacchi Elena , Biemmi Vanessa , Galati Salvatore , Staedler Claudio , Ambrosini Roberto , Kaelin‐Lang Alain 
Published: October 2018

AbstractObjectiveAutonomic nervous system is involved at the onset of Parkinson disease (PD), and alpha‐synuclein (α‐Syn) and its phosphorylated form (p‐αSyn) have been detected in dermal autonomic nerve fibers of PD. We assessed disease specific conformation variant of α‐Syn immunoreactivity in cutaneous nerves and characterized skin denervation patterns in PD and atypical parkinsonism (AP).MethodsWe enrolled 49 subjects, 19 with PD, 17 age‐matched healthy controls, and 13 with AP. The manifestations of disease were rated on clinical scales. Skin biopsies from ankle, thigh, and neck were analyzed by immunofluorescence for p‐αSyn, 5G4 as a conformation specific antibody to pathogenic α‐Syn and PGP9.5 as axonal marker. Intraepidermal nerve fiber density was measured in all anatomical sites as marker of neurodegeneration. Thirteen of the 19 PD underwent a 1 year follow‐up visit plus skin biopsies.ResultsPD subjects displayed more severe cervical skin denervation (P < 0.03), which correlated to disease duration and worsened between initial and follow‐up examination (P < 0.001). p‐αSyn and 5G4 were equally sensitive and specific for the diagnosis of PD (area under the ROC was 0.839 for p‐αSyn and 0.886 for 5G4). PD and AP with possible alpha‐synucleinopathies share the features of marked cervical denervation and the presence of 5G4. In contrast AP with possible tauopathies were normal.InterpretationConformational specific forms of α‐Syn are detectable in skin biopsy by immunofluorescence in PD, with a promising diagnostic efficiency similar to p‐αSyn. Cervical cutaneous denervation correlates with disease duration and increases over time standing out as a potential biomarker of PD progression.
Long‐Term Impact of Belimumab on Health‐Related Quality of Life and Fatigue in Patients With Systemic Lupus Erythematosus: Six Years of Treatment
Authors: Strand Vibeke , Berry Pamela , Lin Xiwu , Asukai Yumi , Punwaney Rajesh , Ramachandran Sulabha 
Published: October 2018

ObjectiveTo report long‐term health‐related quality of life (HRQoL) and fatigue outcomes in patients with systemic lupus erythematosus (SLE) receiving belimumab.MethodsPatients with SLE who completed the Study of Belimumab in Subjects with SLE 76‐week trial (BLISS‐76) were enrolled in this continuation study (BEL112233 [ClinicalTrials.gov identifier: NCT00724867]). The belimumab groups continued to receive the same dose (1 mg/kg or 10 mg/kg) intravenously. After March 2011, all patients received belimumab 10 mg/kg every 28 days plus standard therapy. The placebo group switched to belimumab 10 mg/kg. HRQoL and fatigue assessments included the Short Form 36 (SF‐36) health survey and the Functional Assessment of Chronic Illness Therapy (FACIT)–Fatigue subscale. Post hoc subgroup analyses (BEL206350) assessed clinical characteristics associated with improved HRQoL and fatigue.ResultsOf the 268 patients enrolled, 140 completed the study. Patients receiving long‐term belimumab treatment reported continued improvements in HRQoL and fatigue. At study year 6, the mean ± SD SF‐36 physical component summary (PCS) score and the mental component summary (MCS) score increased from 37.0 ± 9.9 at baseline to 41.7 ± 10.0 (mean ± SD change 4.8 ± 9.4) and from 44.3 ± 11.3 to 47.0 ± 11.6 (mean ± SD change 2.7 ± 11.3) for the PCS and MCS, respectively, exceeding the minimum clinically important difference (MCID) for improvement (2.5 units). The mean ± SD FACIT–Fatigue score exceeded the MCID of 4 at study years 1–5; at study year 6, the mean ± SD change was 3.7 ± 11.8. Statistically significant associations were observed between parent trial treatment groups and change from baseline in PCS, MCS, and FACIT–Fatigue scores (P < 0.01).ConclusionLong‐term control of SLE disease activity with belimumab plus standard therapy translates into meaningful improvements in patient‐reported fatigue and HRQoL.
Incipient Metals: Functional Materials with a Unique Bonding Mechanism
Authors: Wuttig Matthias , Deringer Volker L. , Gonze Xavier , Bichara Christophe , Raty Jean‐Yves 
Published: October 2018

AbstractWhile solid‐state materials are commonly classified as covalent, ionic, or metallic, there are cases that defy these iconic bonding mechanisms. Phase‐change materials (PCMs) for data storage are a prominent example: they have been claimed to show “resonant bonding,” but a clear definition of this mechanism has been lacking. Here, it is shown that these solids are fundamentally different from resonant bonding in the π‐orbital systems of benzene and graphene, based on first‐principles data for vibrational, optical, and polarizability properties. It is shown that PCMs and related materials exhibit a unique mechanism between covalent and metallic bonding. It is suggested that these materials be called “incipient metals,” and their bonding nature “metavalent”. Data for a diverse set of 58 materials show that metavalent bonding is not just a superposition of covalent and metallic cases, but instead gives rise to a unique and anomalous set of physical properties. This allows the derivation of a characteristic fingerprint of metavalent bonding, composed of five individual components and firmly rooted in physical properties. These findings are expected to accelerate the discovery and design of functional materials with attractive properties and applications, including nonvolatile memories, thermoelectrics, photonics, and quantum materials.
Chiral Upconversion Heterodimers for Quantitative Analysis and Bioimaging of Antibiotic‐Resistant Bacteria In Vivo
Authors: Sun Maozhong , Qu Aihua , Hao Changlong , Wu Xiaoling , Xu Liguang , Xu Chuanlai , Kuang Hua 
Published: October 2018

AbstractHeterodimers of upconversion nanoparticles (UCNPs) and gold yolk–shell nanoparticles are fabricated for the quantification of polymyxin‐B‐resistant Escherichia coli. They produce two signals, circular dichroism (CD) and upconversion luminescence (UCL). Interestingly, due to the different affinity of polymyxin B for sensitive and resistant strain, as the concentration of polymyxin B increases, the amount of UCNPs in sensitive bacteria increases sharply, increasing the intracellular UCL signal at a low polymyxin B concentration immobilized on the UCNP. The CD intensity is correspondingly reduced as the amount of UCNPs in solution decreased. Meanwhile, for polymyxin‐B‐resistant strain, the intracellular UCL increases slowly even in a high polymyxin B concentration, and the CD intensity in solution is also enhanced because of the inefficient entering of UCNP. Therefore, based on the concentration of polymyxin B coupled to the UCNPs, the levels of polymyxin‐B‐resistant bacteria can be detected with dual signals. Importantly, with 980 nm irradiation, both polymyxin‐B‐sensitive strains and polymyxin‐resistant bacteria used to induce infection in mice are detected with UCL imaging in vivo and treated well with photodynamic therapy. This novel dual‐mode heterodimer has potential utility for the advanced surveillance and control of drug‐resistant bacteria.