Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of a Segmentation-Free Deep Learning Algorithm for Diagnosing Glaucoma From Optical Coherence Tomography Scans.

Importance Conventional segmentation of the retinal nerve fiber layer (RNFL) is prone to errors that may affect the accuracy of spectral-domain optical coherence tomography (SD-OCT) scans in detecting glaucomatous damage. Objective To develop a segmentation-free deep learning (DL) algorithm for assessment of glaucomatous damage using the entire circle B-scan image from SD-OCT. Design, Setting, and Participants This cross-sectional study at a single institution used data from SD-OCT images of eyes with glaucoma (perimetric and preperimetric) and normal eyes. The data set was randomly split at the patient level into a training (50%), validation (20%), and test data set (30%). Data were collected from March 2008 to April 2019, and analysis began April 2018. Exposures A convolutional neural network was trained to discriminate glaucomatous from normal eyes using the SD-OCT circle B-scan without segmentation lines. Main Outcomes and Measures The ability to discriminate glaucoma from healthy eyes was evaluated by comparing the area under the receiver operating characteristic curve and sensitivity at 80% or 95% specificity for the DL algorithm's predicted probability of glaucoma vs conventional RNFL thickness parameters given by SD-OCT software. The performance was also assessed in preperimetric glaucoma, as well as by visual field severity using Hodapp-Parrish-Anderson criteria. Results A total of 20 806 SD-OCT images from 1154 eyes of 635 individuals (612 [53%] with glaucoma and 542 normal eyes [47%]) were included. The mean (SD) age at SD-OCT scan was 70.8 (10.4) years in individuals with glaucoma and 55.8 (14.1) years in controls. There were 187 women (53.3%) in the glaucoma group and 165 (59.8%) in the control group. Of 612 eyes with glaucoma, 432 (70.4%) had perimetric and 180 (29.6%) had preperimetric glaucoma. The DL algorithm had a significantly higher area under the receiver operating characteristic curve than global RNFL thickness (0.96 vs 0.87; difference = 0.08 [95% CI, 0.04-0.12]) and each RNFL thickness sector for discriminating between glaucoma and controls (all P < .001). At 95% specificity, the DL algorithm (81%; 95% CI, 64%-97%) was more sensitive than global RNFL thickness (67%; 95% CI, 58%-76%). The areas under the receiver operating characteristic curve were also significantly greater for the DL algorithm compared with RNFL thickness at each stage of disease, especially preperimetric and mild perimetric glaucoma. Conclusions and Relevance A segmentation-free DL algorithm performed better than conventional RNFL thickness parameters for diagnosing glaucomatous damage on OCT scans, especially in early disease. Future studies should investigate how such an approach contributes to diagnostic decisions when combined with other relevant clinical information, such as risk factors and perimetry results.
Sexual Shame in the Sexual Excitation and Inhibition Propensities of Men With and Without Nonconsensual Sexual Experiences

ABSTRACT For men with nonconsensual sexual experience (NSEs) histories, sexual shame may play a critical role in their sexual responses. Through online surveys, the current study examined sexual shame in the sexual excitation and inhibition responses of men with NSE histories who both do (identifiers; n = 255) and do not identify (non-identifiers; n = 239) their NSEs with sexual violence labels (e.g., rape) and men with no NSEs (n = 289). Regardless of identification, men with NSEs reported greater sexual shame than men with no NSEs and higher levels of excitatory (e.g., arousability) and inhibitory (e.g., inhibitory cognitions) domains of sexual response propensities. Sexual shame predicted inhibitory domains of sexual response for all of the men. NSE history and identification moderated the relationship between sexual shame and arousability. Sexual shame had a stronger positive association with arousability for both identifiers and those with no NSEs than non-identifiers. The results provide support for the role of sexual shame in men’s sexual response and suggest sexual shame is an important target for interventions with men with NSEs.
Nutritional improvement is associated with better functional outcome in stroke rehabilitation: A cross-sectional study using controlling nutritional status.

OBJECTIVE To investigate the relationship between changes in nutritional status and the functional outcome of adult post-stroke patients hospitalized for rehabilitation. DESIGN A cross-sectional study Subjects: Post-stroke patients who were admitted to a convalescent rehabilitation ward. METHODS On admission and discharge, the nutritional status of each subject was assessed using the "controlling nutritional status" system. Activities of daily living were assessed using the Functional Independence Measure (FIM). Patients were divided into 2 categories: (i) those whose nutritional status improved or remained normal during the rehabilitation; and (ii) all others. RESULTS The median age of patients was 65.5 years. Although there were no significant differences between the 2 categories in most characteristics, the FIM efficiency was significantly higher (-0.230 in the improved category and 0.133 in the other; p < 0.001). Multiple linear regression analysis showed that the improved category as a variable was independently associated with greater FIM efficiency (p < 0.001). CONCLUSION Improvement or maintenance of nutritional status was associated with better functional recovery in post-stroke rehabilitation in adult patients of all ages.
Phyllotaxis Turns Over a New Leaf—A New Hypothesis

Phyllotaxis describes the periodic arrangement of plant organs most conspicuously floral. Oscillators generally underlie periodic phenomena. A hypothetical algorithm generates phyllotaxis regulated by the Hechtian growth oscillator of the stem apical meristem (SAM) protoderm. The oscillator integrates biochemical and mechanical force that regulate morphogenetic gradients of three ionic species, auxin, protons and Ca2+. Hechtian adhesion between cell wall and plasma membrane transduces wall stress that opens Ca2+ channels and reorients auxin efflux “PIN” proteins; they control the auxin-activated proton pump that dissociates Ca2+ bound by periplasmic arabinogalactan proteins (AGP-Ca2+) hence the source of cytosolic Ca2+ waves that activate exocytosis of wall precursors, AGPs and PIN proteins essential for morphogenesis. This novel approach identifies the critical determinants of an algorithm that generates phyllotaxis spiral and Fibonaccian symmetry: these determinants in order of their relative contribution are: (1) size of the apical meristem and the AGP-Ca2+ capacitor; (2) proton pump activity; (3) auxin efflux proteins; (4) Ca2+ channel activity; (5) Hechtian adhesion that mediates the cell wall stress vector. Arguably, AGPs and the AGP-Ca2+ capacitor plays a decisive role in phyllotaxis periodicity and its evolutionary origins.
Thymoquinone treatment modulates the Nrf2/HO-1 signaling pathway and abrogates the inflammatory response in an animal model of lung fibrosis

Abstract The present study investigates the therapeutic potential of thymoquinone (TQ) in bleomycin-induced lung fibrosis (BMILF) and elucidates the target-signaling pathway for its effect. Lung fibrosis was induced in rats by a single intra-tracheal instillation of bleomycin (BM) (6.5 U/kg) followed by thymoquinone treatment (10 and 20 mg/kg p.o.) for 28 days. Control rats received saline instead of TQ. Changes in body weight, inflammatory cells count, cytokines levels, and biochemical parameters of the broncho-alveolar lavage fluid (BALF) were recorded. In addition, a histopathology examination and western blotting were performed on lung tissues. BM administration resulted in a significant weight loss, which was ameliorated by TQ treatment. BMILF was associated with a reduction in the antioxidant mechanisms and increased lipid peroxidation. Furthermore, elevated levels of inflammatory cytokines, MMP-7 expression, apoptotic markers (caspase 3, Bax, and Bcl-2), and fibrotic changes including TGF-β and hydroxyproline levels in lung tissues were evident. These abnormalities were diminished with TQ treatment. Likewise, altered total and differential cell count in BALF was significantly improved in rats treated with TQ. TQ also produced a dose-dependent reduction in the expressions of Nrf2, Ho-1 and TGF-β. These results propose that the Nrf2/Ho-1 signaling pathway is a principal target for TQ protective effect against BMILF in rats. Furthermore, TQ decreases inflammatory oxidative stress possibly through the modulation of nuclear factor Kappa-B (NF-κB) and thereby minimization of collagen deposition in the lung. Therefore, TQ can be developed as a potential therapeutic modularity in BMILF for human use.
Physiological factors affecting uptake and translocation of glufosinate.

Glufosinate is considered a contact herbicide due to its fast activity and limited translocation in plants. We used Palmer amaranth (Amaranthus palmeri S. Watson) as a model species to study plant-related factors affecting glufosinate uptake and translocation. Glufosinate uptake increased rapidly during the initial 24 h, achieving maximum uptake from this time on. The rate of uptake saturated with doses higher than 250 M glufosinate, suggesting the involvement of a membrane transporter. When glufosinate concentrations were higher (>1 mM), uptake was a simple diffusion process in favor of a concentration gradient between the inside and the outside of the cells. Glufosinate uptake was inhibited by the presence of glutamine. The fast action of glufosinate did not limit its own translocation. Because glufosinate is highly water soluble, it translocates mostly through the apoplast or the xylem system. Consequently, old leaves tend to accumulate more herbicide than young meristematic leaves.
Long-term survival and prognostic implications of patients with invasive breast cancer in southern Taiwan

Abstract Our objective in this study was to determine the survival rate of patients with invasive breast cancer and identify the prognostic factors related to all-cause mortality during a 10-year follow-up. Analysis was performed on the medical records of 2002 patients newly diagnosed with breast cancer at a medical center in southern Taiwan between 2006 and 2017. The Kaplan–Meier method and Cox regression analysis were used to estimate survival and the independence of prognostic factors associated with all-cause mortality. Among the 2002 patients, 257 expired during the 10-year follow-up period. The overall survival rates were as follows: 3 years (91.1%), 5 years (85.6%), and 10 years (77.9%). The median survival time was 120.41 months (95% confidence interval: 118.48–122.33 months). Older age, pathologic tumor status, regional lymph node metastasis, distant metastasis, grade/differentiation, treatment modalities, and hormone therapy were significantly related to all-cause mortality. This study identified several clinical factors related to all-cause mortality as well as its relationship to distant metastasis and poor differentiation. Early diagnosis and treatment aimed at preventing recurrence are the keys to survival.
Species Composition, Temporal Abundance and Distribution of Insect Captures Inside and Outside Commercial Peanut Shelling Facilities

Insect populations were studied within two commercial peanut shelling facilities located in the southeastern United States. Commercially available pheromone/kairomone-baited dome traps and pheromone-baited flight traps were deployed throughout processing and shipping portions of the shelling plants and serviced weekly over one year. Lasioderma serricorne, Tribolium castaneum, Typhaea stercorea, Carpophilus spp. , Plodia interpunctella and Cadra cautella were the most common captures across locations. Lasioderma serricorne made up 87% and 88% of all captures in dome traps in plants one and two, respectively. While L. serricorne was not captured during the winter months in flight traps, it was captured with near 100% frequency in dome traps, suggesting that populations persisted throughout the year inside the facilities. Tribolium castaneum populations were active year round. Across insect species and trap type, temperature was a significant covariate for explaining variation in insect counts. After accounting for the effect of temperature, there were always more insects captured in the processing portions of the facilities compared to the shipping areas. A negative linear relationship was observed between captures of L. serricorne and T. castaneum and trap distance from in-shell peanuts entering the shelling facilities. Conversely, fungivores were more evenly distributed throughout all parts of the shelling plants. These data suggest that management efforts should be focused where in-shell peanuts enter to reduce breeding and harborage sites for grain feeding insects.
Interlaboratory comparison of heavy metal testing in animal diagnostic specimens and feed using inductively coupled plasma–mass spectrometry

We compared inductively coupled plasma–mass spectrometry (ICP-MS) test results for the analysis of heavy metals (As, Ba, Cd, Hg, Pb, and Se) in pet foods and routine veterinary diagnostic specimens using intralaboratory and interlaboratory comparisons. Four laboratories, 1 principal laboratory and 3 collaborating laboratories, conducted instrument comparison (limit of detection [LOD], limit of quantification [LOQ], and linear dynamic range [LDR] on 24 data sets), in-house method comparison (accuracy and precision on 120 data sets), and interlaboratory comparison (reproducibility on 528 data sets using Horwitz equation analysis). Matrices tested included 2 types of pet food jerky treats (chicken and sweet potato), bovine blood, and bovine liver and kidney. The instrument comparison study confirmed that ICP-MS provided the sensitivity necessary for the analysis of all heavy metals tested at concentrations below the level of concern for routine diagnostic testing. The “in-house” method comparison samples, spiked at low (0.04 µg/g), medium (0.4 µg/g), and high (8.0 µg/g; note: the high validation level spike for mercury was 2 µg/g) concentration levels, indicated that ICP-MS can meet U.S. FDA acceptance criteria for both accuracy (90–105% recovery) and precision (< 6% coefficient of variation). The interlaboratory comparison studies showed that ICP-MS is a reproducible method for the analysis of heavy metals (HorRat value of 0.5–2.0) except for mercury in one laboratory, which used a different sample preparation method (open block rather than microwave digestion). Overall, our study showed that ICP-MS is a reproducible method for the analysis of heavy metals in spite of minor differences in methodology.
Genotoxic Properties of Synthetic Cannabinoids on TK6 Human Cells by Flow Cytometry

Novel Psychoactive Substances (NPS) include several classes of substances such as synthetic cannabinoids (SCBs), an emerging alternative to marijuana, easily purchasable on internet. SCBs are more dangerous than Δ9-Tetrahydrocannabinol as a consequence of their stronger affinities for the CB1 and CB2 receptors, which may result in longer duration of distinct effects, greater potency, and toxicity. The information on SCBs cytotoxicity, genotoxicity, mutagenicity, and long-term effects is scarce. This fact suggests the urgent need to increase available data and to investigate if some SCBs have an impact on the stability of genetic material. Therefore, the aim of the present study was the evaluation of the mutagenic effect of different SCBs belonging to indole- and indazole-structures. The analyzes were conducted in vitro on human TK6 cells and mutagenicity were measured as micronucleus fold increase by flow cytometry. Our results have highlighted, for the first time, the mutagenic capacity of four SCBs, in particular in terms of chromosomal damage induction. We underline the serious potential toxicity of SCBs that suggests the need to proceed with the studies of other different synthetic compounds. Moreover, we identified a method that allows a rapid but effective screening of NPS placed on the market increasingly faster.
Therapeutic Potential of Direct Clearance of the Amyloid-β in Alzheimer’s Disease

Alzheimer’s disease (AD) is characterized by deposition and accumulation of amyloid-β (Aβ) and its corresponding plaques within the brain. Although much debate exists whether these plaques are the cause or the effect of AD, the accumulation of Aβ is linked with the imbalance between the production and clearance of Aβ. The receptor for advanced glycation endproducts (RAGE) facilitates entry of free Aβ from the peripheral stream. Conversely, lipoprotein receptor-related protein 1 (LRP1), located in the abluminal side at the blood–brain barrier mediates the efflux of Aβ. Research on altering the rates of clearance of Aβ by targeting these two pathways has been extensively study. Additionally, a cerebrospinal fluid (CSF) circulation assistant device has also been evaluated as an approach to increase solute concentration in the CSF via mechanical drainage, to allow for removal of Aβ from the brain. Herein, we provide a brief review of these approaches that are designed to re-establish a homeostatic Aβ balance in the brain.
Assessment of the Quality of Polluted Areas in Northwest Romania Based on the Content of Elements in Different Organs of Grapevine (Vitis vinifera L.)

The purpose of this study was to evaluate the environmental quality of polluted areas near the Baia Mare Mining and Smelting Complex for future improvements the quality of the environment in polluted areas, such as the city of Baia Mare and its surroundings. Samples of soil and organs of grapevine (Vitis vinifera L.) were collected from Baia Mare, Baia Sprie and surrounding areas (Simleul Silvaniei) and their content of Cu, Zn, Pb, Cd, Ni, Co, As, Cr, Hg were analyzed. Most soil and plant samples showed higher metal concentrations in Baia Mare and Baia Sprie areas compared to Simleul Silvaniei, exceeding the normal values. The results obtained from the translocation factors, mobility ratio, as well as from Pearson correlation study confirmed that very useful information is recorded in plant organs: root, canes, leaves and fruit. Results also indicated that Vitis vinifera L. has some highly effective strategies to tolerate heavy metal-induced stress, may also be useful as a vegetation protection barrier from considerable atmospheric pollution. At the same time, berries are safe for consumption to a large degree, which is a great advantage of this species.
Identification and Heterologous Expression of the Albucidin Gene Cluster from the Marine Strain Streptomyces Albus Subsp. Chlorinus NRRL B-24108

Herbicides with new modes of action and safer toxicological and environmental profiles are needed to manage the evolution of weeds that are resistant to commercial herbicides. The unparalleled structural diversity of natural products makes these compounds a promising source for new herbicides. In 2009, a novel nucleoside phytotoxin, albucidin, with broad activity against grass and broadleaf weeds was isolated from a strain of Streptomyces albus subsp. chlorinus NRRL B-24108. Here, we report the identification and heterologous expression of the previously uncharacterized albucidin gene cluster. Through a series of gene inactivation experiments, a minimal set of albucidin biosynthetic genes was determined. Based on gene annotation and sequence homology, a model for albucidin biosynthesis was suggested. The presented results enable the construction of producer strains for a sustainable supply of albucidin for biological activity studies.
Betanodavirus and VER Disease: A 30-year Research Review

The outbreaks of viral encephalopathy and retinopathy (VER), caused by nervous necrosis virus (NNV), represent one of the main infectious threats for marine aquaculture worldwide. Since the first description of the disease at the end of the 1980s, a considerable amount of research has gone into understanding the mechanisms involved in fish infection, developing reliable diagnostic methods, and control measures, and several comprehensive reviews have been published to date. This review focuses on host–virus interaction and epidemiological aspects, comprising viral distribution and transmission as well as the continuously increasing host range (177 susceptible marine species and epizootic outbreaks reported in 62 of them), with special emphasis on genotypes and the effect of global warming on NNV infection, but also including the latest findings in the NNV life cycle and virulence as well as diagnostic methods and VER disease control.
Identification of Functional Transcriptional Binding Sites within Chicken Abcg2 Gene Promoter and Screening Its Regulators

Breast cancer resistance protein (BCRP), an ATP-binding cassette (ABC) half transporter encoded by the Abcg2 gene, is reported to influence the pharmacokinetics of substrate drugs during clinical therapy. The aim of this study was to clarify the mechanisms that regulate the transcription of the chicken Abcg2 gene through cloning and characterization of its promoter region. Results showed that the Abcg2 gene is transcribed by a TATA-less promoter with several putative Sp1 sites upstream from two putative CpG islands. A luciferase reporter assay conducted both in chicken leghorn male hepatoma (LMH) cells and chicken primary hepatocytes mapped a basal promoter to nucleotides −110 to +30, which is responsible for the constitutive expression of Abcg2. The 5′-region upstream of the basal promoter was characterized by both positive and negative regulatory domains. Further, using the cell-based reporter gene assay combined with RT-PCR and drug accumulation analysis, we found that four xenobiotics, daidzein, clotrimazole, ivermectin, and lipopolysaccharide (LPS), influence the expression and function of BCRP through significant regulation of the Abcg2 gene promoter. Interaction sites with the Abcg2 gene promoter of these four selected regulators were clarified by progressive deletions and mutation assays. This study shed some light on the regulatory mechanisms involved in chicken Abcg2 gene expression and the results may have far-reaching significance regarding the usage and development of veterinary drugs.
The Postoperative Changes of Nasal Septum and Maxilla After Alveolar Bone Grafts in Patients With Unilateral Alveolar Cleft.

BACKGROUND Alveolar clefts give rise to many aesthetic and functional problems among affected patients. Therefore, surgical adjustments of the bony defective anomalies are important. The authors performed secondary bone grafts and analyzed the effects particularly on the nasal septum and maxillary area (midface). METHODS The patients who had alveolar bone grafts were retrospectively reviewed with pre/postoperative 3-dimensional computed tomography; the measurements included distances between the anterior nasal spine (ANS) and the vertical midline, angles between the nasal septum and the transverse line, and angles between the floor of the pyriform aperture and the transverse line. RESULTS A total number of 23 patients were finally included in the study. The mean age of the patients was 9.7 ± 1.95 years (range, 7-14 years). The mean distance between the ANS and the vertical midline was 5.3 ± 4.70 mm/4.9 ± 4.15 mm pre/postoperatively, showing the mean paired difference of 0.4 ± 0.89 mm (P < 0.05). The mean angles between the nasal septum and the transverse line and between the floor of the pyriform aperture and the transverse line were 64.5 ± 14.69°/65.9 ± 13.73° and 21.7 ± 8.94°/11.5 ± 7.03° pre/postoperatively, showing the mean paired differences of -1.4 ± 2.78° and 10.1 ± 8.20°, respectively (both P < 0.05). CONCLUSION The results suggest that secondary alveolar bone grafting has expanded effects on the adjacent midfacial structures.