Miracle-dz/UniFAR-FTUs huggingface dataset:
Two New and Nontoxigenic Pseudo‐nitzschia species (Bacillariophyceae) from Chinese Southeast Coastal Waters

To explore the species diversity and toxin profile of Pseudo‐nitzschia, monoclonal strains were established from Chinese southeast coastal waters. The morphology was examined under light and transmission electron microscopy. The internal transcribed spacer region of ribosomal DNA was sequenced for phylogenetic analyses, and the secondary structure of ITS2 was predicted and compared among allied taxa. A combination of morphological and molecular data showed the presence of two new species, Pseudo‐nitzschia hainanensis sp. nov. and Pseudo‐nitzschia taiwanensis sp. nov. Pseudo‐nitzschia hainanensis was characterized by a dumpy‐lanceolate valve with slightly blunt apices and a central nodule, as well as striae comprising two rows of poroids. Pseudo‐nitzschia taiwanensis was characterized by a slender‐lanceolate valve, and striae comprising one row of split poroids. The poroid structure mainly comprised two sectors. Both taxa constituted their own monophyletic lineage in the phylogenetic analyses inferred from ITS2 rDNA and were well differentiated from other Pseudo‐nitzschia species. Morphologically, P. hainanensis and P. taiwanensis could be assigned to the Pseudo‐nitzschia delicatissima and the Pseudo‐nitzschia pseudodelicatissima complex, respectively. Particulate domoic acid was measured using liquid chromatography coupled with tandem mass spectrometry (LC‐MS/MS), but no detectable pDA was found. With the description of the two new species, the species diversity of genus Pseudo‐nitzschia reaches 58 worldwide, among which 31 have been recorded from Chinese coastal waters.
Experimental yellow fever virus infection in the squirrel monkey (Saimiri spp.) I: gross anatomical and histopathological findings in organs at necropsy

BACKGROUND Non-human primates contribute to the spread of the yellow fever virus (YFV) and the establishment of transmission cycles in endemic areas. OBJECTIVE To describe the severe histopathological aspects of YFV infection, 10 squirrel monkeys were infected with YFV and blood, brain, liver, kidney, spleen, heart, lung, lymph node and stomach were collected at 1-7, 10, 20 and 30 days post-infection (dpi). METHODS Histopathological analysis and detection of the genome and viral antigens and neutralising antibodies were performed by RT-PCR, immunohistochemistry and neutralisation test, respectively. FINDINGS Only one animal died from the experimental infection. The genome and viral antigens were detected in all investigated organs (1-30 dpi) and the neutralising antibodies from seven to 30 dpi. The brain contained perivascular haemorrhage (6 dpi); in the liver, midzonal haemorrhage and lytic necrosis (6 dpi) were observed. The kidney had bleeding in the Bowman’s capsule and tubular necrosis (6 dpi). Pyknotic lymphocytes were observed in the spleen (1-20 dpi), the lung had haemorrhage (2-6 dpi), in the endocardium it contained nuclear pyknosis and necrosis (2-3 dpi) and the stomach contained blood in the lumen (6 dpi). MAIN FINDINGS Squirrel monkeys reliably reproduced the responses observed in human cases of yellow fever and, therefore, constitute an excellent experimental model for studies on the pathophysiology of the disease.
The HITSZ TTS system for Blizzard challenge 2020

In this paper, we present the techniques that were used in HITSZ-TTS 1 entry in Blizzard Challenge 2020. The corpus released to the participants this year is about 10-hours speech recordings from a Chinese male speaker with mixed Mandarin and English speech. Based on the above situation, we build an end to end speech synthesis system for this task. It is divided into the following parts: (1) the front-end module to analyze the pronunciation and prosody of text; (2) The phoneme-converted tool; (3) The forward-attention based sequence-to-sequence acoustic model with jointly learning with prosody labels to predict 80-dimensional Mel-spectrogram; (4) The Parallel WaveGAN based neural vocoder to reconstruct waveforms. This is the first time for us to join the Blizzard Challenge, and the identifier for our system is G. The evaluation results of subjective listening tests show that the proposed system achieves unsatisfactory performance. The problems in the system are also discussed in this paper.
Evidence of Industry Scale Effects on Audit Hours, Billing Rates, and Pricing:

Using a proprietary dataset consisting of all private firm audit engagements in 2000 from one Big 4 firm in Belgium, we investigate: (1) whether audit office industry scale is associated with a reduction of total, partner and staff audit hours and thus with efficiency gains triggered by organizational learning from servicing more clients in an industry; and (2) whether the extent of efficiency pass-on from the auditor to its clients depends on the audit firm’s market power. We find that auditor office industry scale is associated with efficiency gains and a reduction of the variable costs (i.e., fewer total audit hours, partner hours, and staff hours), ceteris paribus. Our results also suggest that, on average, realized efficiencies are entirely passed on as evidenced by a non-significant effect of auditor industry scale on the auditor’s billing rate. Furthermore, we find that the extent of the efficiency pass-on decreases with the market power of the audit firm in the industry market segment as we document a higher billing rate for auditors with high market power (versus low market power). In addition, we find that the lower audit hours associated with auditor industry scale do not compromise audit quality.
Transcriptome dynamics in developing leaves from C3 and C4 Flaveria species reveal determinants of Kranz anatomy

C4 species have evolved more than 60 times independently from C3 ancestors. This multiple and parallel evolution of the complex C4 trait indicates common underlying evolutionary mechanisms that might be identified by comparative analysis of closely related C3 and C4 species. Efficient C4 function depends on a distinctive leaf anatomy that is characterized by enlarged, chloroplast rich bundle sheath cells and a narrow vein spacing. To elucidate molecular mechanisms generating this so called Kranz anatomy, we analyzed a developmental series of leaves from the C4 plant Flaveria bidentis and the closely related C3 species Flaveria robusta using leaf clearing and whole transcriptome sequencing. Applying non-negative matrix factorization on the data identified four different zones with distinct transcriptome patterns in growing leaves of both species. Comparing these transcriptome patterns revealed an important role of auxin metabolism and especially auxin homeostasis for establishing the high vein density typical for C4 leaves.
Isolation and Characterization of Sucrose Transporter cDNAs in Cassava

Sucrose transporters (SUTs) play a crucial role in the distribution of photoassimilated carbon in the form of sucrose throughout plants. We took an initial step toward elucidating their role in carbohydrate partitioning in cassava (Manihot esculenta Crantz) by screening both storage root and leaf cDNA libraries for cDNAs encoding SUT type 1, 2 and 4. A full-length cDNA, MeSUT2, was identified in the leaf cDNA library and shared 76% similarity to Citrus sinensis CsSUT2. The fulllength MeSUT1 and MeSUT4 cDNAs, which were isolated from the storage root cDNA library, showed the highest similarity to Ricinus communis RcScr1 (85%) and RcSUC4 (90%), respectively. The translated peptides of all three cassava SUT cDNAs compose of 12 membrane spanning domains and contain conserved motifs [KR]-X-G-R-[KR] for sugar transporters between the second and third transmembrane domains. The asparagine residues for possible N-glycosylation were observed in all MeSUTs. Genomic Southern blot analysis using the cDNA fragments unique to MeSUT1, MeSUT2 and MeSUT4 as probes indicated the presence of more than one copy of each gene in cassava genome.
Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli

The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira . Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.
Isolation, Characterization and Bioactive Properties of Alkali-Extracted Polysaccharides from Enteromorpha prolifera

Four new purified polysaccharides (PAP) were isolated and purified from the Enteromorpha prolifera by alkali extraction, and further characterization was investigated. Their average molecular weights of PAP-1, PAP-2, PAP-3, and PAP-4 were estimated as 3.44 × 104, 6.42 × 104, 1.20 × 105, and 4.82 × 104 Da, respectively. The results from monosaccharide analysis indicated that PAP-1, PAP-2, PAP-3 were acidic polysaccharides and PAP-4 was a neutral polysaccharide. PAP-1 and PAP-2 mainly consist of galacturonic acid, while PAP-3 and PAP-4 mainly contained rhamnose. Congo red test showed that no triple helical structure was detected in the four polysaccharides. The antioxidant activities were investigated using 1,1-diphenyl-2-picrylhydrazyl (DPPH), Superoxide, and 2, 2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical assay. In vitro antitumor activities were evaluated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. PAP-1 exhibited relatively stronger antioxidant activities among the four polysaccharides in a dose-dependent manner. At a concentration of 1.00 mg/mL, the antioxidant activities of PAP-1 on the DPPH radical scavenging rate, superoxide anion radical scavenging rate, and ABTS radical rate at 1.00 mg/mL were 56.40%, 54.27%, and 42.07%, respectively. They also showed no significant inhibitory activity against MGC-803, HepG2, T24, and Bel-7402 cells. These investigations of polysaccharides provide a scientific basis for the use of E. prolifera as an ingredient in functional foods and medicines.
Comparing fetal biometric growth velocity versus estimated fetal weight for prediction of neonatal small for gestational age

Abstract Objective Growth velocities derived from fetal biometrics have been proposed to improve prediction of small for gestational age (SGA) neonates. We sought to determine if ultrasound growth velocities for abdominal circumference (AC) and estimated fetal weight (EFW) improve the prediction of SGA infants when compared to using EFW alone. Study design This is a secondary analysis from a prospective study of women referred for growth ultrasounds during the third trimester. Growth velocities for AC and EFW were derived from the difference in Z-scores between measurements at the anatomy survey (18–22 weeks gestation) and later growth ultrasound (26–36 weeks gestation). Change in AC and EFW growth velocities <10th percentile were compared with prenatally suspected SGA from Hadlock EFW <10th percentile for prediction of SGA neonates. The primary outcome was defined as the sensitivity and specificity of the growth velocities and Hadlock EFW in predicting SGA neonates. Logistic regression modeling was used to determine if the growth velocities improved prediction of neonatal SGA. Area under the ROC curves (AUC) were determined and compared. Results Of 612 singleton pregnancies meeting inclusion criteria, 68 (11.1%) resulted in SGA neonates. Hadlock EFW <10th percentile had higher sensitivity and specificity when compared to AC growth velocity and EFW growth velocity. Only AC growth velocity and Hadlock EFW had significant odds ratios for association with neonatal SGA. The AUC were 0.54, 0.53, and 0.61 using AC growth velocity, EFW growth velocity, and Hadlock EFW, respectively. The AUC did not significantly improve when the growth velocities were combined with Hadlock EFW (0.63). Adjustment of Z-scores for gestational age at anatomy scan or third trimester growth scan did not significantly change these results (AUC = 0.69). Conclusion EFW determined by Hadlock formula has the highest predictive value in detecting SGA neonates when compared to both AC and EFW growth velocities.
Gene expression profile of lipopolysaccharide-induced apoptosis of nucleus pulposus cells reversed by syringic acid

Apoptosis of nucleus pulposus (NP) cells has an important role in the process of intervertebral disc degeneration (IDD), and the search for novel compounds to prevent apoptosis from occurring is urgently required. In the present study, syringic acid (SyrA) was found to exhibit no cytotoxicity on NP cells, and was able to reverse the cytotoxicity, as well as the abnormal expression of Bcl-2 and caspase-3, that were induced by lipopolysaccharide (LPS). The transcriptomes of each group were then analyzed using RNA-Seq. A total of 65 differentially expressed genes (DEGs) were identified in LPS-stimulated groups (LPS group vs. control group), 819 DEGs were identified in the SyrA-reversed groups (SyrA plus LPS group vs. LPS group), and a further 25 DEGs were identified in the SyrA plus LPS group compared with the control group. Reverse transcription-quantitative PCR validation indicated that the alterations in expression of uroplakin 3B-like 1 (UPK3BL1), voltage-dependent calcium channel subunit α-2/δ-1 (CACNA2D1) and polo-like kinase 4 (PLK4) were consistent with the corresponding results of RNA-Seq, and that these genes were involved in both LPS-stimulation and SyrA-reversion processes. Kyoto Encyclopedia of Genes and Genomes analyses indicated that the DEGs in SyrA-reversed groups were involved in, amongst other pathways, ‘Autophagy-other’ and ‘Apoptosis-multiple species’. In conclusion, the addition of SyrA to the NP cells co-incubated with LPS appeared to help prevent the abnormal expression of mRNAs and apoptosis that had been identified in NP cells incubated with LPS alone. The potential mechanism underlying the reversion of SyrA might be attributed to the regulation of CACNA2D1 and PLK4.
Predictive Value of Serum Ferritin in Combination with Alanine Aminotransferase and Glucose Levels for Noninvasive Assessment of NAFLD: Fatty Liver in Obesity (FLiO) Study

The identification of affordable noninvasive biomarkers for the diagnosis and characterization of nonalcoholic fatty liver disease (NAFLD) is a major challenge for the research community. This study aimed to explore the usefulness of ferritin as a proxy biomarker of NAFLD condition, alone or in combination with other routine biochemical parameters. Subjects with overweight/obesity and ultrasound-confirmed liver steatosis (n = 112) from the Fatty Liver in Obesity (FLiO) study were assessed. The hepatic evaluation considered magnetic resonance imaging, ultrasonography, and credited routine blood liver biomarkers. Anthropometry and body composition, dietary intake (by means of a validated 137-item food frequency questionnaire), and specific biochemical markers were also determined. Serum ferritin levels were analyzed using a chemiluminescent microparticle immunoassay kit. Lower serum ferritin concentrations were associated with general better liver health and nutritional status. The evaluation of ferritin as a surrogate of liver damage by means of quantile regression analyses showed a positive association with alanine aminotransferase (ALT) (β = 19.21; p ≤ 0.001), liver fat content (β = 8.70; p = 0.008), and hepatic iron (β = 3.76; p ≤ 0.001), after adjusting for potential confounders. In receiver operating characteristic (ROC) analyses, the panel combination of blood ferritin, glucose, and ALT showed the best prediction for liver fat mass (area under the curve (AUC) 0.82). A combination of ferritin and ALT showed the higher predictive ability for estimating liver iron content (AUC 0.73). This investigation demonstrated the association of serum ferritin with liver health as well as with glucose and lipid metabolism markers in subjects with NAFLD. Current findings led to the identification of ferritin as a potential noninvasive predictive biomarker of NAFLD, whose surrogate value increased when combined with other routine biochemical measurements (glucose/ALT).
Transcatheter mitral valve thrombosis: A case report and literature review

Transcatheter mitral valve replacement (TMVR) is an exciting alternative therapy for complex patients with mitral valve disease. Experience with TMVR is new and there is a lot yet to discover about their durability, long‐term outcomes, and complications including mitral transcatheter heart valve (THV) thrombosis. Many factors have been speculated to increased risk of THV thrombosis. Here, we report a case of a 72‐year‐old woman who developed mitral THV thrombosis after undergoing TMVR for severe mitral regurgitation with mitral annular calcification. We reviewed 42 TMVR papers with 1,484 patients, including 60 with mitral THV thrombosis. We discussed the most common strategies used for mitral THV thromboprophylaxis and treatment.
Use of Patient-Reported Symptoms from an Online Symptom Tracking Tool for Dementia Severity Staging: Development and Validation of a Machine Learning Approach

Background SymptomGuide Dementia (DGI Clinical Inc) is a publicly available online symptom tracking tool to support caregivers of persons living with dementia. The value of such data are enhanced when the specific dementia stage is identified. Objective We aimed to develop a supervised machine learning algorithm to classify dementia stages based on tracked symptoms. Methods We employed clinical data from 717 people from 3 sources: (1) a memory clinic; (2) long-term care; and (3) an open-label trial of donepezil in vascular and mixed dementia (VASPECT). Symptoms were captured with SymptomGuide Dementia. A clinician classified participants into 4 groups using either the Functional Assessment Staging Test or the Global Deterioration Scale as mild cognitive impairment, mild dementia, moderate dementia, or severe dementia. Individualized symptom profiles from the pooled data were used to train machine learning models to predict dementia severity. Models trained with 6 different machine learning algorithms were compared using nested cross-validation to identify the best performing model. Model performance was assessed using measures of balanced accuracy, precision, recall, Cohen κ, area under the receiver operating characteristic curve (AUROC), and area under the precision-recall curve (AUPRC). The best performing algorithm was used to train a model optimized for balanced accuracy. Results The study population was mostly female (424/717, 59.1%), older adults (mean 77.3 years, SD 10.6, range 40-100) with mild to moderate dementia (332/717, 46.3%). Age, duration of symptoms, 37 unique dementia symptoms, and 10 symptom-derived variables were used to distinguish dementia stages. A model trained with a support vector machine learning algorithm using a one-versus-rest approach showed the best performance. The correct dementia stage was identified with 83% balanced accuracy (Cohen κ=0.81, AUPRC 0.91, AUROC 0.96). The best performance was seen when classifying severe dementia (AUROC 0.99). Conclusions A supervised machine learning algorithm exhibited excellent performance in identifying dementia stages based on dementia symptoms reported in an online environment. This novel dementia staging algorithm can be used to describe dementia stage based on user-reported symptoms. This type of symptom recording offers real-world data that reflect important symptoms in people with dementia.
Differential Expression Profiling Reveals Stress-Induced Cell Fate Divergence in Soybean Microspores

Stress-induced microspore embryogenesis is a widely employed method to achieve homozygosity in plant breeding programs. However, the molecular mechanisms that govern gametophyte de- and redifferentiation are understood poorly. In this study, RNA-Seq was used to evaluate global changes across the microspore transcriptome of soybean (Glycine max [L.] Merrill) as a consequence of pretreatment low-temperature stress. Expression analysis revealed more than 20,000 differentially expressed genes between treated and control microspore populations. Functional enrichment illustrated that many of these genes (e.g., those encoding heat shock proteins and cytochrome P450s) were upregulated to maintain cellular homeostasis through the mitigation of oxidative damage. Moreover, transcripts corresponding to saccharide metabolism, vacuolar transport, and other pollen-related developmental processes were drastically downregulated among treated microspores. Temperature stress also triggered cell wall modification and cell proliferation—characteristics that implied putative commitment to an embryonic pathway. These findings collectively demonstrate that pretreatment cold stress induces soybean microspore reprogramming through suppression of the gametophytic program while concomitantly driving sporophytic development.
External root resorption in root-filled and vital teeth after extraction and non-extraction orthodontic treatments: a split-mouth retrospective study

Abstract Objective This study aimed to compare the amounts of external root resorption (ERR) during different modalities of orthodontic treatment (OT) in root-filled teeth (RFT) and their contralateral teeth with vital pulp (VPT) in the same patient. Material and methods The study sample consisted of 69 patients in two groups: 35 patients in the non-extraction group (18 female, 17 male; 18.16 ± 3.79 years), and 34 patients in the extraction group (19 female, 15 male; 17.72 ± 2.78 years). Digital panoramic radiographs of each patient taken before and after OT were used to measure the tooth length and root surface area. The amounts of ERR in RFT and contralateral VPT were evaluated pre- and post-OT in mandibular molars. The data were statistically analyzed with the paired t-test, independent t-test, and analysis of covariance (ANCOVA) (p < .05). Results A statistically significant difference was observed in both the orthodontic treatment groups when RFT and VPT were compared in terms of ERR (p < .05). A significant difference was observed between RFT and VPT in extraction treatments when the reduction in the root area between the two sides in the groups was compared (p < .05). Conclusions RFT are more resistant to ERR than VPT. The ERR in RFT may not be a significant matter for the planning of OT.