Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on features of water environment in industrialized shrimp culture system

The features of water environment in an industrialized shrimp culture system were studied by in-situ experiment, and comparative analyses were carried out to reveal the significant difference between industrialized aquaculture and outdoor aquaculture systems. The results showed that:(1) the water environment in an industrialized shrimp culture ecosystem had the following features: the temperature, salinity and dissolved oxygen content in the culture water could be manually controlled. The variation scales of pH and Chl-a could be controlled temporarily, but not in the long run. However, the variation of nutrients could not be manually controlled. (2) Compared with outdoor pond shrimp culture, the fluctuation of temperature, salinity and dissolved oxygen content in the industrialized culture water was less, and their mean values were significantly lower (P0.001). At the same time, the variation of pH were greater, and the mean value was significantly higher (P0.001). The Chl-a content was maintained at a high level and without obvious difference compared to that of outdoor pond shrimp culture. The range of nutrient content fluctuation was at low levels, and there were no significant difference (P0.001). Between the two culture models, in which the NO3-N was the major form of nitrogen (the percentage of NO3-N in the whole dissolved inorganic nitrogen was 62.7%); and none of the contents of NH4-N、NO2-N、NO3-N and PO4-P were affected by the contents of DO and/or shrimp culture densities, which was similar to outdoor pond shrimp culture. (3) The industrialized shrimp culture system was a fragile ecosystem in which the channels of energy and matter were narrower and simpler than those of outdoor pond shrimp culture system. However, this ecosystem was an active ecosystem, and signified by features such as low nutrient contents, swift nutrient circulation and high productivity, which were similar to those in the outdoor pond shrimp culture system.
2D CNN versus 3D CNN for false-positive reduction in lung cancer screening

Abstract. Purpose: To clarify whether and to what extent three-dimensional (3D) convolutional neural network (CNN) is superior to 2D CNN when applied to reduce false-positive nodule detections in the scenario of low-dose computed tomography (CT) lung cancer screening. Approach: We established a dataset consisting of 1600 chest CT examinations acquired on different subjects from various sources. There were in total 18,280 candidate nodules in these CT examinations, among which 9185 were nodules and 9095 were not nodules. For each candidate nodule, we extracted a number of cubic subvolumes with a dimension of 72 × 72 × 72 mm3 by rotating the CT examinations randomly for 25 times prior to the extraction of the axis-aligned subvolumes. These subvolumes were split into three groups in a ratio of 8 ∶ 1 ∶ 1 for training, validation, and independent testing purposes. We developed a multiscale CNN architecture and implemented its 2D and 3D versions to classify pulmonary nodules into two categories, namely true positive and false positive. The performance of the 2D/3D-CNN classification schemes was evaluated using the area under the receiver operating characteristic curves (AUC). The p-values and the 95% confidence intervals (CI) were calculated. Results: The AUC for the optimal 2D-CNN model is 0.9307 (95% CI: 0.9285 to 0.9330) with a sensitivity of 92.70% and a specificity of 76.21%. The 3D-CNN model with the best performance had an AUC of 0.9541 (95% CI: 0.9495 to 0.9583) with a sensitivity of 89.98% and a specificity of 87.30%. The developed multiscale CNN architecture had a better performance than the vanilla architecture did. Conclusions: The 3D-CNN model has a better performance in false-positive reduction compared with its 2D counterpart; however, the improvement is relatively limited and demands more computational resources for training purposes.
The Relationship between Extracellular/intracellular microRNAs and TLRs May Be Used as a Diagnostic and Therapeutic Approach in Sepsis

ABSTRACT One of the leading causes of death in the intensive care unit (ICU) is sepsis. Different studies have been performed on different markers to determine the cause of sepsis. microRNAs (miRNAs) are non-coding RNAs that can be released both inside and outside the cell and regulate the target gene expression by binding to the 3ʹ untranslated region (3ʹUTR) of the target genes. TLRs play an important role in innate immunity that can be modulated by biological markers such as microRNAs. In this study, we summarized the recent progress on the role of extracellular and intracellular microRNAs in sepsis. It has also been focused on the association of TLRs with extracellular and intracellular micro RNAs in the regulation of sepsis. In conclusion, this study has provided new insight into the role of microRNAs as a regulator of the TLRs which may lead to the aberrant inflammatory response in sepsis. Therefore, it suggests that both intracellular and extracellular microRNAs may play a therapeutic role in the treatment of sepsis via regulating TLRs. However, yet sepsis and septic shock are medical emergencies and further studies are needed to specify the exact role of microRNAs and TLRs in sepsis.
Oogenesis in hydra. II. Cytophotometric determination of DNA concentration in the nuclei of somatic and sex cells

: During sexual reproduction in Hydra, interstitial cells in the female sex zone of the body (i-cells) undergo mitotic division and form a thickening in the epiderm. The proliferation of i-cells is accompanied by the increase of cytoplasm volume and by the appearance in the cytoplasm of a great number of membranous structures (rough endoplasmic reticulum, Golgi apparatus and mitochondria), enzymatic granules, lipid inclusions and glycogen. All cells of the epidermal thickening soon (in approximately twenty four hours) acquire the characteristics of typical phagocytes. However it is the cell situated inside the group of syncytially connected ones and adjacent to mesogloea that begins to grow rapidly and phagocytize surrounding cells. The cells of the epidermal thickening, though they are often given the name of oogonia, were found to have a tetraploid DNA content in their nuclei. The presence of four unseparated centrioles of equal size suggests that all preparatory processes for division were completed. A conclusion was drawn that cells of the epidermal thickening undergo premeiotic DNA synthesis prior to their phagocytizing by the growing oocyte and, thus, are oocytes themselves. The oogonial stage in Hydra coincides with the early period of mitotic reproduction of i-cells. The data obtained are discussed from the viewpoint of the formation of the accessory gonad apparatus.
A switchable ceramide transfer protein for dissecting the mechanism of ceramide‐induced mitochondrial apoptosis

Mitochondrial translocation of ceramides triggers Bax‐dependent apoptosis. To elucidate how ceramides activate Bax and commit cells to death, we developed a switchable version of the ceramide transfer protein CERT, sCERT. Upon its drug‐induced recruitment to mitochondria, sCERT retains the ability to bind VAP proteins in the ER and catalyzes mitochondrial import of externally added fluorescent ceramides. Mitochondrial recruitment of sCERT also triggers mitochondrial translocation of Bax. The ability of mitochondria‐bound sCERT to mediate ceramide import and Bax translocation requires both its START domain and ongoing ceramide biosynthesis. These data extend our previous finding that mistargeting of ER ceramides to mitochondria specifically activates Bax and establish sCERT as a novel tool to dissect the underlying mechanism in a time‐resolved manner.
Rapid Eye Movement Sleep Sawtooth Waves Are Associated with Widespread Cortical Activations

Sawtooth waves (STW) are bursts of frontocentral slow oscillations recorded in the scalp electroencephalogram (EEG) during rapid eye movement (REM) sleep. Little is known about their cortical generators and functional significance. Stereo-EEG performed for presurgical epilepsy evaluation offers the unique possibility to study neurophysiology in situ in the human brain. Sawtooth waves (STW) are bursts of frontocentral slow oscillations recorded in the scalp electroencephalogram (EEG) during rapid eye movement (REM) sleep. Little is known about their cortical generators and functional significance. Stereo-EEG performed for presurgical epilepsy evaluation offers the unique possibility to study neurophysiology in situ in the human brain. We investigated intracranial correlates of scalp-detected STW in 26 patients (14 women) undergoing combined stereo-EEG/polysomnography. We visually marked STW segments in scalp EEG and selected stereo-EEG channels exhibiting normal activity for intracranial analyses. Channels were grouped in 30 brain regions. The spectral power in each channel and frequency band was computed during STW and non-STW control segments. Ripples (80-250 Hz) were automatically detected during STW and control segments. The spectral power in the different frequency bands and the ripple rates were then compared between STW and control segments in each brain region. An increase in 2-4 Hz power during STW segments was found in all brain regions, except the occipital lobe, with large effect sizes in the parietotemporal junction, the lateral and orbital frontal cortex, the anterior insula, and mesiotemporal structures. A widespread increase in high-frequency activity, including ripples, was observed concomitantly, involving the sensorimotor cortex, associative areas, and limbic structures. This distribution showed a high spatiotemporal heterogeneity. Our results suggest that STW are associated with widely distributed, but locally regulated REM sleep slow oscillations. By driving fast activities, STW may orchestrate synchronized reactivations of multifocal activities, allowing tagging of complex representations necessary for REM sleep-dependent memory consolidation. SIGNIFICANCE STATEMENT Sawtooth waves (STW) present as scalp electroencephalographic (EEG) bursts of slow waves contrasting with the low-voltage fast desynchronized activity of REM sleep. Little is known about their cortical origin and function. Using combined stereo-EEG/polysomnography possible only in the human brain during presurgical epilepsy evaluation, we explored the intracranial correlates of STW. We found that a large set of regions in the parietal, frontal, and insular cortices shows increases in 2-4 Hz power during scalp EEG STW, that STW are associated with a strong and widespread increase in high frequencies, and that these slow and fast activities exhibit a high spatiotemporal heterogeneity. These electrophysiological properties suggest that STW may be involved in cognitive processes during REM sleep.
Competition alters tree growth responses to climate at individual and stand scales

Understanding how climate affects tree growth is essential for assessing climate change impacts on forests but can be confounded by effects of competition, which strongly influences tree responses to climate. We characterized the joint influences of tree size, competition, and climate on diameter growth using hierarchical Bayesian methods applied to permanent sample plot data from the montane forests of Mount Rainier National Park, Washington State, USA, which are mostly comprised of Abies amabilis Douglas ex Forbes, Tsuga heterophylla (Raf.) Sarg. , Pseudotsuga menziesii (Mirb.) Franco, and Thuja plicata Donn ex D. Don. Individual growth was sensitive to climate under low but not high competition, likely because tree ability to increase growth under more favorable climates (generally greater energy availability) was constrained by competition, with important variation among species. Thus, climate change will likely increase individual growth most in uncrowded stands with lower competition. However, crowde.
Accurate segmentation of prostate cancer histomorphometric features using a weakly supervised convolutional neural network

Prostate cancer (PCa) arises from the glandular epithelium. To confirm the presence of cancer, a pathologist uses stained tissue samples taken either from biopsy or prostatectomy. Due to the relationship between epithelium and cancer, special consideration is given to regions identified as epithelium. Histomophometric techniques have long been used to identify areas of epithelium within the tissue for automated detection and classification pipelines; however, they are often rigid in their implementation and their performance suffers on large datasets where variation in staining, imaging, and preparation is difficult to control. The recent development and popularity of deep learning methods for image processing and segmentation offer great promise for developing robust classification pipelines for such ends; however, they require large labeled datasets for training.
The γ-Protocadherins Regulate the Survival of GABAergic Interneurons during Developmental Cell Death

Inhibitory interneurons integrate into developing circuits in specific ratios and distributions. In the neocortex, inhibitory network formation occurs concurrently with the apoptotic elimination of a third of GABAergic interneurons. The cell surface molecules that select interneurons to survive or die are unknown. Here, we report that members of the clustered Protocadherins (cPCDHs) control GABAergic interneuron survival during developmentally-regulated cell death. Conditional deletion of the gene cluster encoding the γ-Protocadherins (Pcdhgs) from developing GABAergic neurons in mice of either sex causes a severe loss of inhibitory populations in multiple brain regions and results in neurologic deficits such as seizures. By focusing on the neocortex and the cerebellar cortex, we demonstrate that reductions of inhibitory interneurons result from elevated apoptosis during the critical postnatal period of programmed cell death (PCD). By contrast, cortical interneuron (cIN) populations are not affected by removal of Pcdhgs from pyramidal neurons or glial cells. Interneuron loss correlates with reduced AKT signaling in Pcdhg mutant interneurons, and is rescued by genetic blockade of the pro-apoptotic factor BAX. Together, these findings identify the PCDHGs as pro-survival transmembrane proteins that select inhibitory interneurons for survival and modulate the extent of PCD. We propose that the PCDHGs contribute to the formation of balanced inhibitory networks by controlling the size of GABAergic interneuron populations in the developing brain. SIGNIFICANCE STATEMENT A pivotal step for establishing appropriate excitatory-inhibitory ratios is adjustment of neuronal populations by cell death. In the mouse neocortex, a third of GABAergic interneurons are eliminated by BAX-dependent apoptosis during the first postnatal week. Interneuron cell death is modulated by neural activity and pro-survival pathways but the cell-surface molecules that select interneurons for survival or death are unknown. We demonstrate that members of the cadherin superfamily, the clustered γ-Protocadherins (PCDHGs), regulate the survival of inhibitory interneurons and the balance of cell death. Deletion of the Pcdhgs in mice causes inhibitory interneuron loss in the cortex and cerebellum, and leads to motor deficits and seizures. Our findings provide a molecular basis for controlling inhibitory interneuron population size during circuit formation.
Stability of ectromelia virus strain NIH-79 under various laboratory conditions.

: Ectromelia virus strain NIH-79 was suspended in fetal bovine serum (FBS), minimum essential medium, Hanks' base plus 10% FBS (MEMH + FBS), phosphate-buffered saline (PBS) or PBS plus 50% glycerol (PBS + G). Suspensions were held as liquids or as dry spots at various temperatures. Virus was most stable in FBS and least stable in PBS + G at 4 degrees C, room temperature (23-25 degrees C) or 37 degrees C. Virus held at 4 degrees C was more stable than virus held at higher temperatures, irrespective of supporting medium. Dried spots of blood or serum from ectromelia virus-infected mice remained infectious at room temperature for 11 days and 4 days, respectively. Dried spots of FBS that contained virus were infectious for 5 days, whereas virus retained infectivity for 1 day after drying in other media. Virus was inactivated completely in 10% serum in PBS exposed to 60 degrees C for 30 minutes. Virus was inactivated completely in slices of infected liver and spleen immersed in 10% neutral buffered formalin for 20 hours. These results show that the stability of ectromelia virus strain NIH-79 is medium and temperature dependent and that rapid inactivation occurs after treatments routinely used in diagnostic and research procedures.
Membrane-bound hemichrome in density-separated cohorts of normal (AA) and sickled (SS) cells.

: The presence of bound heme pigment was compared in membranes of AA and SS cells. Spectophotometric study of membranes prepared by hypotonic lysis and washed free of hemoglobin revealed the presence of an irreversibly oxidized hemoglobin derivative, HCh. SS cell membranes contained significantly more HCh than did the AA cell membranes. When red cells were separated into cohorts of various density on a discontinuous density gradient of Stractan, washed membranes from the highest-density AA cells had significantly more HCh than did the remainder. In contrast, when density-separated SS cells were studied, no significant difference could be demonstrated in the HCh content of membranes from various cohorts.
EnDPoINT: protocol for an implementation research study to integrate a holistic package of physical health, mental health and psychosocial care for podoconiosis, lymphatic filariasis and leprosy into routine health services in Ethiopia

Introduction Neglected tropical diseases (NTDs) causing lower limb lymphoedema such as podoconiosis, lymphatic filariasis (LF) and leprosy are common in Ethiopia. Routine health services for morbidity management and disability prevention (MMDP) of lymphoedema caused by these conditions are still lacking, even though it imposes a huge burden on affected individuals and their communities in terms of physical and mental health, and psychosocial and economic outcomes. This calls for an integrated, holistic approach to MMDP across these three diseases. Methods and analysis The ‘Excellence in Disability Prevention Integrated across NTDs’ (EnDPoINT) implementation research study aims to assess the integration and scale-up of a holistic package of care—including physical health, mental health and psychosocial care—into routine health services for people with lymphoedema caused by podoconiosis, LF and leprosy in selected districts in Awi zone in the North–West of Ethiopia. The study is being carried out over three phases using a wide range of mixed methodologies. Phase 1 involves the development of a comprehensive holistic care package and strategies for its integration into the routine health services across the three diseases, and to examine the factors that influence integration and the roles of key health system actors. Phase 2 involves a pilot study conducted in one subdistrict in Awi zone, to establish the care package’s adoption, feasibility, acceptability, fidelity, potential effectiveness, its readiness for scale-up, costs of the interventions and the suitability of the training and training materials. Phase 3 involves scale-up of the care package in three whole districts, as well as its evaluation in regard to coverage, implementation, clinical (physical health, mental health and psychosocial) and economic outcomes. Ethics and dissemination Ethics approval for the study has been obtained in the UK and Ethiopia. The results will be disseminated through publications in scientific journals, conference presentations, policy briefs and workshops.
Prostate Cancer Incidence and Survival, by Stage and Race/Ethnicity — United States, 2001–2017

Among U.S. men, prostate cancer is the second leading cause of cancer-related death (1). Past studies documented decreasing incidence of prostate cancer overall since 2000 but increasing incidence of distant stage prostate cancer (i.e., signifying spread to parts of the body remote from the primary tumor) starting in 2010 (2,3). Past studies described disparities in prostate cancer survival by stage, age, and race/ethnicity using data covering ≤80% of the U.S. population (4,5). To provide recent data on incidence and survival of prostate cancer in the United States, CDC analyzed data from population-based cancer registries that contribute to U.S. Cancer Statistics (USCS). * Among 3.1 million new cases of prostate cancer recorded during 2003-2017, localized, regional, distant, and unknown stage prostate cancer accounted for 77%, 11%, 5%, and 7% of cases, respectively, but the incidence of distant stage prostate cancer significantly increased during 2010-2017. During 2001-2016, 10-year relative survival for localized stage prostate cancer was 100%. Overall, 5-year survival for distant stage prostate cancer improved from 28.7% during 2001-2005 to 32.3% during 2011-2016; for the period 2001-2016, 5-year survival was highest among Asian/Pacific Islanders (API) (42.0%), followed by Hispanics (37.2%), American Indian/Alaska Natives (AI/AN) (32.2%), Black men (31.6%), and White men (29.1%). Understanding incidence and survival differences by stage, race/ethnicity, and age can guide public health planning related to screening, treatment, and survivor care. Future research into differences by stage, race/ethnicity, and age could inform interventions aimed at improving disparities in outcomes.
Evaluation of antimicrobial efficacy of quaternized poly[bis(2-chloroethyl)ether-alt-1,3-bis[3-(dimethylamino)propyl]urea] against targeted pathogenic and multi-drug-resistant bacteria

Here, we have investigated in vitro antimicrobial efficacy of a quaternized cationic polymer, poly[bis(2-chloroethyl)ether-alt-1,3-bis[3-(dimethylamino)propyl]urea] (polyquaternium-2), against gram-positive as well as gram-negative bacteria along with several multi-drug-resistant bacterial strains. The antimicrobial efficacy of this polymer was first tested against some clinical pathogens followed by microorganisms isolated from acne lesions. Interestingly, polyquaternium-2 exhibited significant antimicrobial activity against methicillin-resistant Staphylococcus aureus, for which very limited drugs are available. Most importantly, the polymer displayed low haemolytic activity and non-toxic behaviour against mammalian cells. The results showed the promising potential of the projected polymer to be utilized as an antibacterial agent for various biomedical applications.