Miracle-dz/UniFAR-FTUs huggingface dataset:
Dense reconstruction of brain-wide neuronal population close to the ground truth

Recent progresses allow imaging specific neuronal populations at single-axon level across mouse brain. However, digital reconstruction of neurons in large dataset requires months of human labor. Here, we developed a tool to solve this problem. Our tool offers a special error-screening system for fast localization of submicron errors in densely packed neurites and along long projection across the whole brain, thus achieving reconstruction close to the ground-truth. Moreover, our tool equips algorithms that significantly reduce intensive manual interferences and achieve high-level automation, with speed 5 times faster compared to semi-automatic tools. We also demonstrated reconstruction of 35 long projection neurons around one injection site of a mouse brain at an affordable time cost. Our tool is applicable with datasets of 10 TB or higher from various light microscopy, and provides a starting point for the reconstruction of neuronal population for neuroscience studies at a single-cell level.
Patient Factors Linked with Return Acute Healthcare Use in Older Adults by Discharge Disposition

Compare patient characteristics by hospital discharge disposition (home without services, home with home healthcare (HHC) services, or post‐acute care (PAC) facilities). Examine timing and rates of 30‐day healthcare utilization (rehospitalization, emergency department (ED) visit, or observation (OBS) visit) and patient characteristics associated with rehospitalization by discharge location.
Adaptation of diet in a changed environment: Increased consumption of lobster krill Munida gregaria (Fabricius, 1793) by Argentine hake

Fil: Belleggia, Mauro. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Subsede Instituto Nacional de Investigacion y Desarrollo Pesquero; Argentina
APC/C Cdh1-mediated degradation of Cdh1 during meiosis in S. cerevisiae

The Anaphase-Promoting Complex/Cyclosome (APC/C) is a ubiquitin ligase that promotes the ubiquitination and subsequent degradation of numerous cell cycle regulators during mitosis and in G1. Proteins are recruited to the APC/C by activator proteins such as Cdh1. During the cell cycle, Cdh1 is subject to precise regulation so that substrates are not degraded prematurely. We have explored the regulation of Cdh1 during the developmental transition into meiosis and sporulation in the budding yeast S. cerevisiae. Transition to sporulation medium triggers the degradation of Cdh1. Degradation requires that cells be of the a/a mating type and be starved for glucose, but they do not actually need to enter into the meiotic program. Degradation requires an intact SNF1 protein kinase complex (orthologous to the mammalian AMPK nutritional sensor), which is activated by the absence of glucose. Cdh1 degradation is mediated by the APC/C itself in a ‘trans’ mechanism in which one molecule of Cdh1 recruits a second molecule of Cdh1 to the APC/C for ubiquitination. However, Cdh1-Cdh1 recognition does not depend on the degradation motifs or binding sites involved in the recognition of typical APC/C substrates. We hypothesize that Cdh1 degradation is necessary for the preservation of cell cycle regulators and chromosome cohesion proteins between the reductional and equational meiotic divisions, which occur without the intervening Gap or S phases found in mitotic cell cycles.
Study of hormone levels and semen parameters in infertile patients and fertile controls from Batna

Background: Male infertility or the inability of a man to procreate is a major public health problem and is a leading cause of marital discord in countries such as Algeria. Endocrine disorders that can be associated with significant medical pathology remain an important factor to be considered in the etiology of male infertility, and those disorders are usually associated with alteration of sperm count or in severe cases with azoospermia. In this study, we are evaluating semen parameters and hormonal levels of patients with idiopathic male infertility and comparing their results with healthy fertile controls. Methods: We aim to study the impact of hormones; follicle stimulating hormone (FSH), luteinizing hormone (LH), testosterone (T) and prolactin (PRL) on idiopathic male fertility and their impact on semen parameters, we conducted a study on 71 male subjects with 39 infertile men and 32 fertile controls from the city of Batna (Algeria). Our study lasted six months and was conducted at the University Hospital of Batna and a private analysis laboratory. Results: The results of semen analysis allowed us to determine that the most common pathology in our population is OANTS with a percentage of 21.05% followed by NS and NT with 13.16%; results of the permocytogramme show a predominance of atypical forms of the head with a frequency of 39.21%. Regarding the hormone dosage, prolactin was the most disturbed hormone with an average value of (18 Â± 6.221 ng/ml), which is almost pathologic; the other hormones showed some disturbances but to a lesser degree. The results of spermiologique parameters of infertile men compared with fertile controls showed highly significant differences (Pâ‰¤O.OOO1) regarding motility, concentration vitality, and spermatozoa morphology. The comparison of results of hormones between the two groups revealed differences in LH and prolactin levels; no differences were found regarding FSH and testosterones. Concerning the relationship between hormones and spermiologiques parameters, positive correlations were found between (LH and sperm concentration) (testosterone and sperm concentration), and, finally, a strong correlation was found between the levels of prolactin and the anomalies of intermediate piece of spermatozoa. Conclusion: This study showed that hormonal disorders are not a common cause of male infertility in our study population. It further showed the relative frequencies of the various semen abnormalities during the study period. Also, we found associations between altered semen parameters and pathological levels of some hormones; however, a complementary study with a more subjects is needed.
Stress, life history and dental development : a histological study of mandrills (Mandrillus sphinx)

Dental development is frequently used to reconstruct life history in primates for which little other information exists. In addition to the regular growth increments visible in histological tooth sections, accentuated lines are thought to form at the time of stressful events in the lives of individual animals. However, our understanding of when, how and why such accentuated lines form in relation to stressful events is limited. In this thesis, I tested the hypothesis that accentuated lines in the enamel and dentine are associated with stressful events in the lives of semi-free-ranging mandrills (Mandrillus sphinx, Cercopithecidae) from the Centre International de Recherches Medicales de Franceville, Gabon. I used dates of birth and death to calibrate dental histology to calendar time and individual age. I then reconstructed dental development sequences for individual mandrills, providing a detailed overview of mandrill dental development. I report sex-specific dental development chronologies, crown extension rates and stages of dental development, and compare these to mandrill life history. Based on this dental development data, I matched the observed accentuated lines in the mandrill teeth with the dates of events in the mandrills’ lives. My results suggest that accentuated lines can correspond to potentially stressful events, including resumption of reproductive cycling in the mother and menstrual cycles, and in some occasions with parturitions. My results show that male mandrills might form accentuated lines at the time of potentially stressful events too, but most potentially stressful life history events for males take place after dental development is complete. Furthermore, my findings suggest that the number of accentuated lines recorded in teeth varies between individuals in a population, reflecting differences that may influence reproductive success.
Genetic Engineering of the Oleaginous Yeast Trichosporon oleaginosus and the Bacteria Escherichia coli Aimed at the Production of High Value Lipids and Bioactive Diterpenes

The current Ph.D. thesis consists of two independent parts. The primary section covers establishment of genetic engineering tools and targeted metabolic engineering of the non-conventional oleaginous yeast Trichosporon oleaginosus to generate non-native fatty acids. The fermentative production of these non-native lipids was evaluated based on cheap, renewable carbon sources. The second part of the theses covers the targeted engineering of the bacterial diterpene synthase CotB2 to generate novel diterpene macrocycles. Moreover, Escherichia coli was metabolically engineered to produce the tri-hydroxylated diterpene Cyclooctatin, using a newly identified reductase/ferredoxin system from Streptomyces. afghaniensis (AfR•Afx). The molecular basis for the activity of the AfR•Afx system was elucidated.
Characterization of the Nuclear Export Signal of Human Papillomavirus 16 L2 Minor Capsid Protein

3-4 Acknowledgements.5-6 Abbreviations.7 List of Figures.8 Introduction.9-14 Materials and Methods.15-17 Results.18 Discussion.19-20 Figures.21-33 References.34-35
Whole genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s

Salmonella enterica serovar Enteritidis (SE), the most commonly reported serovar of human salmonellosis, has been frequently associated with poultry farms, eggs and egg products. Mice are known vectors of SE contamination in these facilities. The objective of this study was to use whole-genome sequencing (WGS) to analyze SE from mice obtained at poultry farms in Pennsylvania. Documenting pathogen diversity can identify reliable biomarkers for rapid detection and speed up outbreak investigations. We sequenced 91 SE isolates from 83 mice (62 spleen isolates, 29 intestinal isolates) caught at 15 poultry farms between 1995-1998 using an Illumina NextSeq 500. We identified 742 single nucleotide polymorphisms (SNPs) capable of distinguishing each isolate from one another. Isolates were divided into two major clades: there were more SNPs differences within Clade B than counterparts in Clade A. All isolates containing antimicrobial resistance genes belong to Subgroup B2. Clade-defining SNPs provided biomarkers distinguishing isolates from 12 individual subgroups, which were separated by farm location or year of collection. Nonsynonymous changes from the clade-defining SNPs proffered a better understanding of possible genetic variations among these isolates. For a broader view of SE diversity, we included data from NCBI Pathogen Detection Isolates Browser, in which subgroups in Clade B formed new SNP Clusters. Importance WGS and SNPs analyses are excellent and powerful tools for investigating SE phylogenies. Identifying the evolutionary relationships among SE isolates from mouse, poultry, environmental, and clinical isolates, along with patterns of genetic diversity, advances understanding of SE and the role mice may play in SE contamination and spread among poultry population. Our data was able to identify SE isolates from different farms or years of collection. Moreover, the annotations of clade-defining SNPs provided information about possible protein functions among these SE isolates from each subgroup. Clade-defining or farm-unique biomarkers were useful for rapid detection and outbreak investigations.
Study on the Interaction of Retinoic Acids to Human Serum Albumin by Fluorescence and Circular Dichroism Spectroscopy

Retinoic acids (RAs) are considered to be endocrine disruptor chemicals and toxic environmental priority pollutants. In this paper, the interactions between RAs and human serum albumin (HSA) were examined by steady state fluorescence, time-resolved fluorescence and circular dichroism spectroscopy (CD). The RAs quenched the fluorescence of the protein remarkably and the mechanism of quenching was found to be static in nature. Synchronous fluorescence studies suggested that the polarity around the tryptophan(Trp) residues and tyrosine(Tyr) residues was not altered in the presence of RAs. The thermodynamic parameters of the binding reactions (ΔGθ, ΔHθ, ΔSθ) were measured,and they indicated the presences of hydrophobic forces and hydrogen interactions in the RAs–HSA interactions. The alterations of HSA secondary structure in the presence of RAs were confirmed by CD and time resolved fluorescence spectroscopy.
Karakteristik Nanoemulsi Ekstrak Kulit Buah Manggis (Garcinia Mangostana L.)

Penggunaan ekstrak kulit buah manggis secara langsung dapat menimbulkan ketidaknyamanan dan memiliki ukuran partikel besar sehingga penetrasi dan absorpsinya pada kulit kurang baik, untuk itu dibuat dalam bentuk nanoemulsi dengan Self Nanoemulsifying Drug Delivery System untuk aplikasi topikal. Penggunaan nanoemulsi pada kulit dapat meningkatkan penetrasi dan absorpsi bahan aktif melalui kulit tanpa perlu menambahkan eksipien penetrasi lain dan memiliki luas permukaan yang besar sehingga lebih efektif sebagai sistem pembawa. Penelitian ini bertujuan untuk mengetahui karakteristik ektrak etil asetat kulit buah manggis yang dikorporasikan kedalam bentuk nanoemulsi dan untuk mengetahui sifat fisika sediaan nanoemulsi. Nanoemulsi dibuat dengan komposisi Virgin Coconut Oil sebagai fase minyak, Etanol 96% sebagai kosurfaktan, Cremofor RH 40 sebagai surfaktan, dan aqua deion sebagai fase air dengan perbandingan 1:7:2:5, kemudian campuran tersebut distirrer dan disonikasi lalu dilakukan pengujian stabilits fisik dan diukur nilai persen transmitan pada panjang gelombang 650 nm dengan spektrofotometri UV-Vis. Didapatkan hasil analisis keseluruh formula nanoemulsi, semakin banyak jumlah ekstrak kulit buah manggis yang diinkorporasikan ke dalam fase minyak, maka warna nanoemulsi yang terbentuk semakin pekat dan nilai persen trasmitan yang dihasilkan juga akan semakin kecil.
Use of Noncoding Plastid Marker trnL-F as DNA Barcode for Identification of True Mangrove Genus Rhizophora

DNA barcoding should provide rapid, accurate identifications by using a standardized DNA region. The ability to discriminate all species is the ultimate target in barcoding. The barcoding method has been extremely useful in species identification, cryptic species identification, biodiversity studies, forensic analysis and phylogenetics. Application of DNA barcoding to plants has primarily focused on evaluating the success of candidate barcodes across a broad spectrum of evolutionary divergence. In addition to accurately identifying query sequences, results showed that DNA barcoding is useful for detecting taxonomic uncertainty, determining whether erroneous taxonomy. The magnitude of differentiation within and among the Rhizophora species sampled suggests that our results inform how DNA barcoding will perform among closely related species in genera.
Cloning, Expression and Enzymatic Characterization of Chitin Deacetylase 4 from Hyphantria Cunea (Drury)

A novel chitin deacetylase (CDA), HcCDA4, was identified from the American white moth, Hyphantria cunea. The full-length cDNA sequence of HcCDA4 was identified,and the cDNA is 1494bp in length. The HcCDA4 was shown as a 56 kDa protein in E. coli BL21 by SDS-PAGE analysis and the specific antibodies reacting to HcCDA4 were obtained by immunizing rabbits. The insect cells secreting expressed HcCDA4 proteins were used to study enzymatic properties. Results showed that HcCDA4 possessed catalytic activity, and the optimum temperature was 50oC and the optimum pH was 8.0. Under the optimum reaction conditions, the enzyme activities of HcCDA4 protein was 3.44 -1 U mL  . The enzyme activity is enhanced in the presence of 2 Zn  , 2 Mn  and 2 Fe  ions, but inhibited in the presence of 2 Mg  and 2 Co  ions, 2+ Ca showed a trend of increasing first and then decreasing on HcCDA4 enzymatic activity.
Development of fluorescent biosensors and inhibitors to probe and target CDK5/p25 in glioblastoma

CDK5 is a protein kinase ubiquitously expressed but mainly activated in the central nervous system, where it plays an important role in neuronal functions such as synaptic transmission, axonal guidance and migration, synaptic plasticity and neuronal development. CDK5 is associated with p35 protein at the cell membrane, then activated by calpain-mediated cleavage of p35 into p25, which promotes relocalization of CDK5/p25 into the cytoplasm. CDK5/p25 phosphorylates a wide variety of substrates including Tau, thereby contributing to appearance of neurofibrillary plaques responsable for neurodegenerative pathologies such as comme Alzheimer’s et Parkinson’s, when hyperactivated. More recent studies suggest that CDK5 expression and hyperactivation are involved in glioblastoma during cell invasion and CDK5 expression has been reported to be correlated with the pathological grade of gliomas. However there are currently no tools available to monitor CDK5/p25 activity in its native cellular environment, in tissues or in tumours, due to an overall lack of reliable tools to quantify dynamic changes in its kinase activity in a sensitive and continuous fashion. Furthermore, few inhibitors are currently available to target CDK5/p25 in a specific fashion and most of them are ATP competitive inhibitors.The first goal of my thesis was to develop a fluorescent peptide biosensor named CDKACT5, that specifically reports on recombinant CDK5/p25 and on endogenous CDK5 activity in cell extracts in a dynamic and reversible fashion following stimulation or inhibition of this kinase. Once validated in vitro, this biosensor was applied to detect alterations in CDK5/p25 activity in different glioblastoma cell lines in fluorescent kinase activity assays. Finally CDKACT5 was introduced into cultured neuronal cells to monitor dynamic changes in CDK5/p25 activity by fluorescence imaging and time-lapse microscopy.The second goal of my thesis project consisted in developing a conformational fluorescent biosensor to identify non-ATP competitive inhibitors targeting the activation loop of CDK5. CDKCONF5 was implemented to perform a high throughput screen of three small molecule libraries. The hits identified were validated and characterized to determine their inhibitory potential in kinase activity and proliferation assays, as well as their mechanism of action. These compounds constitute promising for selective chemotherapy in glioblastoma.
The Design and Preliminary Evaluation of a Mobile Health Application TangTangQuan in Management of Type 1 Diabetes in China

Objective: To assess the effectiveness of mobile health application TangTangQuan (TTQ) in management of type 1 diabetes (T1D) in China. Methods: TTQ is designed to provide diabetes self-management education (DSME) for patients with T1D.The innovation of TTQ is to break the isolation of individual T1D patients by socializing their self-management data, and let them find the “patients like me. ” TTQ included four major modules: personal diabetes diary, games for DSME, peer support communities and online education courses. Patients recorded and uploaded their diabetes diary via TTQ, and peer patients or family members were able to make comments, or share their own experiences, or interact with the up loaders under the posts. Free download and registration of TTQ was available in major APP stores for mobiles in China since September 2015. The self-report demographic and clinical data were collected through TQQ. Results: During September 2015 and December 2017, a total of 7641 patients (M/F, 3716/3925) aged 21.28±14.43 years, with duration of T1D 2.50 (1.00,6.90) years, have signed up and joined the management of TTQ, from 21 provinces in China. Fifty two percent were 18 to 45 years old and 41% were less than 18 years old. Twenty four percent of them were active in peer support communities including sharing their experiences in management of T1D. Among 2903 patients with duration of diabetes ≥1 year who have used TTQ for ≥1 year,435 have continuous record for 1 year of self-meter blood glucose (SMBG) at least 4 times per day in TTQ. Among these patients, SMBG frequency was 2.43/week(1.40,13.13) and 2.88/week(0.63,11.92) (P=0.967), HbA1c was 6.59±1.40% and 6.40±1.39%(P=0.002), the frequency of hypoglycemia was 6.75/week (4.00,11.50) and 6.25/week (2.75,9.67) (P=0.005) before and after one year use of TTQ, respectively. Conclusions: TTQ has the potential to be a novel intervention for engaging T1D patients and their families in positive communication to support DSME. Disclosure P. Ling: None. S. Luo: None. J. Yan: None. X. Zheng: None. D. Yang: None. X. Zeng: None. J. Weng: None.
Antibacterial Activity of Some Seaweed Extracts against Multidrug Resistant Urinary Tract Bacteria and Analysis of their Virulence Genes

Worldwide, urinary tract infections (UTI) are among the most common infectious diseases. About 150 million people are diagnosed with UTI every year (Gonzalez and Schaeffer, 1999). A urinary tract infection is an infection involving the kidneys, ureters, bladder, or urethra. These are the structures that urine passes through before being eliminated from the body (Foxman and Brown, 2003). Virtually, an infection occurs when Gram negative bacteria (Escherichia coli, Klebsiella pneumoniae and Proteus vulgaris) get into the urine and begin to grow. The infection usually starts at the opening of the urethra, where the urine leaves the body and moves upward into the urinary tract, these bacteria normally live in the bowel (colon) and around the anus. The symptoms develop rapidly including fairly high fever, shaking chills, nausea and vomiting (Kalaivani et al., 2016). UTI infection may complicate into an acute or chronic kidney infection (pyelonephritis) or even permanent kidney damage due to neglected or not correctly treated infection. Many classes of antibiotics were classified as typical treatments for such diseases. However, the improper and uncontrolled use of many antibiotics resulted in the occurrence of International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 11 (2017) pp. 2569-2586 Journal homepage: http://www.ijcmas. com
Do People and Neural Nets Pay Attention to the Same Words: Studying Eye-tracking Data for Non-factoid QA Evaluation

We investigated how users evaluate passage-length answers for non-factoid questions. We conduct a study where answers were presented to users, sometimes shown with automatic word highlighting. Users were tasked with evaluating answer quality, correctness, completeness, and conciseness. Words in the answer were also annotated, both explicitly through user mark up and implicitly through user gaze data obtained from eye-tracking. Our results show that the correctness of an answer strongly depends on its completeness, conciseness is less important. Analysis of the annotated words showed correct and incorrect answers were assessed differently. Automatic highlighting helped users to evaluate answers quicker while maintaining accuracy, particularly when highlighting was similar to annotation. We fine-tuned a BERT model on a non-factoid QA task to examine if the model attends to words similar to those annotated. Similarity was found, consequently, we propose a method to exploit the BERT attention map to generate suggestions that simulate eye gaze during user evaluation.