Miracle-dz/UniFAR-FTUs huggingface dataset:
Upper Miocene-Lower Pliocene taxonomy and stratigraphy in the circum North Atlantic Basin: radiation and extinction of Amauroliths, Ceratoliths and the D. quinqueramus lineage.

Three Neogene nannofossil lineages evolved rapidly in the Late Miocene to Early Pliocene: the Amauroliths, the Ceratoliths and the Discoaster quinqueramus lineage. The evolution of these lineages has been extensively studied within the petroleum industry, in particular BP America Inc. and its heritage companies, due to their considerable utility in the deep-water Gulf of Mexico. This study presents their biostratigraphic usage and taxonomic concepts for the Upper Miocene-Lower Pliocene interval (NN8-NN14). They are further defined utilizing astronomically “tuned” sediments from Ocean Drilling Program Leg 154 (western equatorial Atlantic), yielding 42 primary calibrated nannfossil events. Based on these results, we divide Zone NN12 (Martini, 1971) into two new Subzones (NN12a & b) and emend its top and base. Additionally, the taxonomy and stratigraphic distribution of Amauroliths, Ceratoliths, and theD. quinqueramus lineage are clarified. Three newAmaurolith and Ceratolith taxa are described, A. brevigracilis, C. apiculus and C. cornulum as well as eleven new species of Discoaster: D. abrachiatus, D. astellaris, D. compactus, D. consutus, D. explicatus, D. gemmulatus, D. hexaramus, D. newellii, D. prolixus, D. tetracladus and D. vinsonii. In addition, several taxa are formally emended.
Variability of External Genetic Characteristic of Kokok Balenggek Chicken in West Sumatera, Indonesia

Kokok Balenggek chicken is one of the rare indigenous chickens in Indonesia. They are unique as they produce a melodious song like crow. They have syllabic diversity, as each portion of the call can be composed with different pitches and vocalizations. The identification and characterizations of local adorn chicken is very important for animal conservation. A research was conducted in west Sumatera to identify the genetic variability of the external genetic characteristic of Kokok Balenggek chicken. This research was conducted in a limited area of Solok district West Sumatera, Indonesia. About 203 (111 males and 92 females) Kokok Balenggek chicken were observed. The varieties are based on base colour of feather, colour of the plumage, flick feather, pattern of feather, shank colour and comb types. The method were used to analyze the rate of purity and native gene, the frequency of autosomal and sex-linked of the genes, feather pattern, rate of introgression from the exotic breed of Rhode Island Red, White Leghorn and of Barred Plymouth Rock. The research showed that the highest controlling genes characteristic external of kokok Balenggek chicken are coloured (ii), wild type pattern (e+), plain feather (ss) golden flick feather (ss), yellow shank coloured (Id_) and single comb (pp). A constitution on external genetic characteristic of Kokok Balenggek is ii e+_bbssId_pp. while The purity gene of Kokok Balenggek chicken has only 45.30%. Its genetic introgression is affected by the exotic breed from Europa and America with genetic introgression value of 0.5470. According to the rate of heterozygosity value of kokok Balenggek chicken varied within 29.41%. In conclusion, the Kokok Balenggek chickens show heterogeneity in the external genetic. To complete a set of their characterization further studies are needed on their quantitative traits and the molecular composition.
The Application of Case Study Evaluations

Rather than using large samples and following a rigid protocol to examine a limited number of variables, case study methods involve an in-depth, longitudinal examination of a single instance or event. It is a systematic way of looking at what is happening, collecting data, analyzing information, and reporting the results. The product is a sharpened understanding of why the instance happened as it did, and what might be important to look at more extensively in future research. Thus, case studies are especially well suited toward generating, rather than testing, hypotheses.
First Report of Pantoea ananatis (Syn. Erwinia uredovora) Being Associated with Peanut Rust in Georgia

Peanut rust (Figs. 1 and 2) and leaf spots are the main foliar fungal diseases of peanut (Arachis hypogaea L). Peanut rust occurs every year in Texas, and sporadically in Alabama (6) and Georgia. Fungicide applications to control peanut leaf spots caused by Cercospora arachidicola Hori and Cercosporidium personatum (Berk & M.A. Curtis) Deighton are also effective against peanut rust. However, untreated, peanut rust could be as devastating as leaf spot diseases (6) causing severe defoliation. To genetically characterize the causal agent of peanut rust, Puccinia arachidis Speg. , we prepared SSR-enriched libraries according to the method of Techen et al. (7) adapted for Nextera kit (Epicentre, Madison, WI) using DNA of urediniospores, and performed highthroughput sequencing with Roche 454 as previously described (2). Surprisingly, after assembling contigs and comparing sequences to databases using BLAST analysis (1), almost half of the contigs had significant similarity (expected values ≤ 1 × 10 ) to the bacterium Pantoea ananatis (Syn. Erwinia uredovora). To confirm the presence of this bacterium, we used urediniospores collected from three locations in Georgia, one from Attapulgus and two from Tifton (Fig. 3). Ten-fold dilutions of P. arachidis urediniospores were made in phosphate-buffer saline (PBS), determined urediniospore number in the suspensions using a haemocytometer, and plated the dilutions onto LuriaBertani (3) Agar plates. Bacterial colonies growing on plates from the Attapulgus sample had the appearance of a pure culture, with yellow-rounded glossy colonies like Erwinia (Fig. 4); these colonies were counted and estimated at 30 cfu per urediniospore. The same type of colonies were observed in the Tifton samples, but at much lower proportion compared to other bacterial species on the Petri dishes. To confirm the identity of the Erwinia-like bacteria growing on Petri dishes, a total of 52 colonies were isolated, including some not similar to Erwinia spp. , and a 1300-bp fragment of their 16S ribosomal-RNA genes was PCR amplified. PCR amplicons were cloned into TOPO4 vector (Invitrogen) and sequenced. BLAST analysis confirmed that colonies resembling Erwinia were indeed P. ananatis. P. ananatis has received many scientific names throughout the years, i.e., Pectobacterium ananas (Serrano), then, renamed as Erwinia uredovora (Pon) Dye 1963 was reported as parasitic of uredia in cereal rust. The term "uredo-vora" means "feeds on uredospores," and in 1975 Hevesi and Mashaal described the mechanism of infection of E. uredovora as a parasite of fungi. The potential of E. uredovora as biological control of rust-producing fungal pathogens, by inhibiting urediniospore germination and lysing spores of Puccinia graminis, P. recondita, P. coronata, and Uromyces appendiculatus was summarized by Gowdu and Balasubramanian (5). Other agricultural -4
Training a computer-aided polyp detection system to detect sessile serrated adenomas using public domain colonoscopy videos

Abstract Background Colorectal cancer (CRC) is a major public health burden worldwide, and colonoscopy is the most commonly used CRC screening tool. Still, there is variability in adenoma detection rate (ADR) among endoscopists. Recent studies have reported improved ADR using deep learning models trained on videos curated largely from private in-house datasets. Few have focused on the detection of sessile serrated adenomas (SSAs), which are the most challenging target clinically. Methods We identified 23 colonoscopy videos available in the public domain and for which pathology data were provided, totaling 390 minutes of footage. Expert endoscopists annotated segments of video with adenomatous polyps, from which we captured 509 polyp-positive and 6,875 polyp-free frames. Via data augmentation, we generated 15,270 adenomatous polyp-positive images, of which 2,310 were SSAs, and 20,625 polyp-negative images. We used the CNN AlexNet and fine-tuned its parameters using 90 % of the images, before testing its performance on the remaining 10 % of images unseen by the model. Results We trained the model on 32,305 images and tested performance on 3,590 images with the same proportion of SSA, non-SSA polyp-positive, and polyp-negative images. The overall accuracy of the model was 0.86, with a sensitivity of 0.73 and a specificity of 0.96. Positive predictive value was 0.93 and negative predictive value was 0.96. The area under the curve was 0.94. SSAs were detected in 93 % of SSA-positive images. Conclusions Using a relatively small set of publicly-available colonoscopy data, we obtained sizable training and validation sets of endoscopic images using data augmentation, and achieved an excellent performance in adenomatous polyp detection.
Colorectal Cancer Detection Based on Deep Learning

Introduction: The initial point in the diagnostic workup of solid tumors remains manual, with the assessment of hematoxylin and eosin (H&E)-stained tissue sections by microscopy. This is a labor-intensive step that requires attention to detail. In addition, diagnoses are influenced by an individual pathologist's knowledge and experience and may not always be reproducible between pathologists. Methods: We introduce a deep learning-based method in colorectal cancer detection and segmentation from digitized H&E-stained histology slides. Results: In this study, we demonstrate that this neural network approach produces median accuracy of 99.9% for normal slides and 94.8% for cancer slides compared to pathologist-based diagnosis on H&E-stained slides digitized from clinical samples. Conclusion: Given that our approach has very high accuracy on normal slides, use of neural network algorithms may provide a screening approach to save pathologist time in identifying tumor regions. We suggest that this new method may be a powerful assistant for colorectal cancer diagnostics.
Portable Nanohybrid Paper-Based Chemiresistive Sensor for Free Chlorine Detection

Detecting the concentration of free chlorine is important for monitoring the quality of water. In this study, we report a nanohybrid paper-based chemiresistive sensor that can be used with smartphones to detect free chlorine ions. The sensor was fabricated using a simple and standardized coating process. The graphene and poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) nanohybrid paper-based sensing device exhibited a more stable and intuitive response to free chlorine than that exhibited by the device using only PEDOT:PSS. The nanohybrid paper-based sensor was sensitive to free chlorine concentrations in a linear range of 0.1–500 ppm, and the limit of detection was 0.18 ppm. The sensor showed specificity for free chloride ions and detection capability in samples. The sensor was integrated as a module with an electric readout system, and the measured signals and results could be displayed in real time on a smartphone. Therefore, the proposed sensing platform is suitable owing to its portability, low cost, ease of use, and capability for on-site water quality measurement.
Double Negative Differential Resistance Device Based on Hafnium Disulfide/Pentacene Hybrid Structure

Recently, combinations of 2D van der Waals (2D vdW) materials and organic materials have attracted attention because they facilitate the formation of various heterojunctions with excellent interface quality owing to the absence of dangling bonds on their surface. In this work, a double negative differential resistance (D‐NDR) characteristic of a hybrid 2D vdW/organic tunneling device consisting of a hafnium disulfide/pentacene heterojunction and a 3D pentacene resistor is reported. This D‐NDR phenomenon is achieved by precisely controlling an NDR peak voltage with the pentacene resistor and then integrating two distinct NDR devices in parallel. Then, the operation of a controllable‐gain amplifier configured with the D‐NDR device and an n‐channel transistor is demonstrated using the Cadence Spectre simulation platform. The proposed D‐NDR device technology based on a hybrid 2D vdW/organic heterostructure provides a scientific foundation for various circuit applications that require the NDR phenomenon.
Weak Data: The Social Biography of a Measurement Instrument and How It Failed to Ensure Accountability in Home Care

Abstract Contemporary health and social care is saturated by processes of datafication. In many cases, these processes are nested within an ostensibly simple logic of accountability: Define a politically and morally desirable goal, then measure the level of achievement. This logic has come to permeate public health initiatives globally and today it operates in most health care systems in various ways. We explore here a particular instantiation of the logic associated with the introduction of a measurement instrument used in Danish home care. Building on ethnographic fieldwork, interviews, and analysis of policy documents, we show how the instigated processes of datafication—despite hopeful political claims—erode care levels and disempower older people. We believe that these findings can be of relevance for other settings that subscribe to the same accountability logic and to similar forms of measurement instruments.
Evaluation of Time Dependent Changes of the Rat's Lung in Experimentally Induced Diabetes Mellitus: Light and Electron Microscopic Study

Introduction: Diabetes mellitus is a chronic metabolic disease characterized by persistent hyperglycemia. It is a major health problem that is associated with a number of serious, sometimes life‐threatening complications. There has been increasing evidence that the respiratory functions of patients with diabetes are impaired in the course of their disease. Aim of the Work: This work aimed to study structural changes of the rat's lung in experimentally induced diabetes and evaluation of these changes in relation to duration of diabetes. Materials and Methods: Thirty adult male albino rats were divided into three groups. Group I served as control group. Group II consisted of two equal subgroups of rats (IIa & IIb), which received citrate buffer. Group III included two equal subgroups (IIIa & IIIb), which were subjected to induction of diabetes by using streptozotocin (STZ). Subgroups IIa & IIIa were sacrificed after four weeks from the experiment while subgroups IIb & IIIb were sacrificed after eight weeks. Blood samples were collected three times during the experiment to measure the blood glucose level. At the end of the experiment, the lungs were dissected out and the specimens were prepared for light and electron microscopic study. Morphometric analysis was also done to confirm the results. Results: After 4 weeks of induction of diabetes, there was significant increase in the thickness of interalveolar septa which showed cellular infiltration. Some bronchioles showed patchy areas of hyperplasia of their lining epithelium. After 8 weeks of induction of diabetes, the lung revealed accumulation of large number of alveolar macrophages and inflammatory cells in the pulmonary interstitium leading to highly significant increase in the thickness of interalveolar septa and collapse of many alveoli with loss of normal architecture of the lung parenchyma. Congestion of the blood vessels and thickening of their walls could be seen with extravasation of RBCs and fluid exudates in the interstitium. There was increased deposition of collagen fibres by increasing duration of diabetes. Electron microscopy revealed significant increase in the mean number of type II pneumocytes which showed progressive degenerative changes with increasing duration of diabetes. Conclusion: It could be concluded that, diabetes induced structural changes of the lung which increased progressively and became much worse with increasing duration of diabetes. So much attention should be directed to early diagnosis and treatment of diabetes to avoid or postpone onset of complications.
A Review of the Impact of Bariatric Surgery in Women With Polycystic Ovary Syndrome

Polycystic ovarian syndrome (PCOS) is the most common endocrine disorder in reproductive-age women that causes infertility. Obesity and insulin resistance are closely tied to the pathophysiology of PCOS. Current first-line treatments include lifestyle modifications, hormone modulators, and laparoscopic ovarian drilling, but little attention has been given to bariatric surgery as a viable option. A detailed review of the literature regarding the outcomes of obese women with PCOS after bariatric surgery is necessary. All studies were found in the PubMed database, limited to females and humans, and selected due to relevancy and quantitative data. Bariatric surgery promotes significant weight loss within one year, which is associated with amelioration of insulin resistance, hyperandrogenism, menstrual irregularity, and ovulatory dysfunction. Surgery successfully mediates the regression of PCOS and promotes successful pregnancy. Thus, we recommend the consideration of bariatric surgery as part of the main treatment considerations in obese patients with PCOS. However, more focused and comprehensive research with better study designs are still needed in the future to investigate PCOS and bariatric surgery.
Safety and Tolerability of Sodium Thiosulfate in Patients with an Acute Coronary Syndrome Undergoing Coronary Angiography: A Dose-Escalation Safety Pilot Study (SAFE-ACS)

Background In animal studies, hydrogen sulfide (H2S) has been shown to protect the heart from ischemia-reperfusion injury. This study evaluates the safety and tolerability of the H2S donor sodium thiosulfate (STS) in patients with acute coronary syndrome (ACS). Methods Eighteen patients, undergoing coronary angiography for ACS, received STS intravenously immediately after arrival at the catheterization laboratory according to a “3 + 3 dose-escalation design” with fixed dosing endpoint (0, 2.5, 5, 10, 12.5, and 15 grams). This first dose STS was combined with verapamil and nitroglycerin required for transradial procedures. A second dose STS was administered 6 hours later. Primary endpoint was dose-limiting toxicity, defined as significant hemodynamic instability or death up to 24 hours or before discharge from the coronary care unit. Secondary outcomes included the occurrence of anaphylaxis, nausea, vomiting, and systolic blood pressure (SBP) course. Results Sixteen patients received two dosages of STS and two patients one dosage. None of the patients reached the primary endpoint, nor experienced a serious adverse event. We observed a clinically well-tolerated decline in SBP 1 hour after administration of the first STS dose and concomitant verapamil/nitroglycerin. SBP for all patients together reduced 16.8 (8.1–25.5) mmHg (P = 0.0008). No significant decline in SBP occurred after the second dose. Mild nausea was observed in one patient. Conclusion This is the first report on sodium thiosulfate administration in patients with acute coronary syndromes. Our data suggest that sodium thiosulfate was well tolerated in this setting. The potential benefit of this intervention has to be examined in larger studies.
Predicting the Real‐Valued Inter‐Residue Distances for Proteins

Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved inter‐residue contact prediction, contact‐based structure prediction has gradually reached the performance ceiling. New methods have been proposed to predict the inter‐residue distance, but unanimously by simplifying the real‐valued distance prediction into a multiclass classification problem. Here, a lightweight regression‐based distance prediction method is shown, which adopts the generative adversarial network to capture the delicate geometric relationship between residue pairs and thus could predict the continuous, real‐valued inter‐residue distance rapidly and satisfactorily. The predicted residue distance map allows quick structure modeling by the CNS suite, and the constructed models approach the same level of quality as the other state‐of‐the‐art protein structure prediction methods when tested on CASP13 targets. Moreover, this method can be used directly for the structure prediction of membrane proteins without transfer learning.
Distinct Age-Dependent C Fiber-Driven Oscillatory Activity in the Rat Somatosensory Cortex

Abstract When skin afferents are activated, the sensory signals are transmitted to the spinal cord and eventually reach the primary somatosensory cortex (S1), initiating the encoding of the sensory percept in the brain. While subsets of primary afferents mediate specific somatosensory information from an early age, the subcortical pathways that transmit this information undergo striking changes over the first weeks of life, reflected in the gradual emergence of specific sensory behaviors. We therefore hypothesized that this period is associated with differential changes in the encoding of incoming afferent volleys in S1. To test this, we compared S1 responses to A fiber skin afferent stimulation and A + C skin afferent fiber stimulation in lightly anaesthetized male rats at postnatal day (P)7, P14, P21, and P30. Differences in S1 activity following A and A + C fiber stimulation changed dramatically over this period. At P30, A + C fiber stimulation evoked significantly larger γ, β, and α energy increases compared with A fiber stimulation alone. At younger ages, the changes in S1 oscillatory activity evoked by the two afferent volleys were not significantly different. Silencing TRPV1+ C fibers with QX-314 significantly reduced the γ and β S1 oscillatory energy increases evoked by A + C fibers, at P30 and P21, but not at younger ages. Thus, C fibers differentially modulate S1 oscillatory activity only from the third postnatal week, well after the functional maturation of the somatosensory cortex. This age-related change in afferent evoked S1 oscillatory activity may underpin the maturation of sensory discrimination in the developing brain.
Analysis of Active Components in Mailuoning Injection by Platelet Membrane Immobilized Chromatography

OBJECTIVE To analysis the effective chemicals in Mailuoning injection by platelet membrane immobilized chromatograghy (PMIC) . METHODS The effective chemicals in Mailuoning injection were combined by the platelet membrane under imitated physical environments. The unattached substances were washed away by the PBS of pH 7.4. Then the attached compounds were eluled by the PBS of pH 4.0. The released compounds from target were collected and analyzed by HPLC.RESULTS Eight characteristic active compounds in the Mailuoning injection were found to bind to the membrane of platelets. CONCLUSION PMIC can be a screening model for the preparations of anti-thromboembolic disease, it can reflect the intensity of the pharmacological action between the compounds and the biological targets in the cell membrane, such as receptors,channels and enzymes etc.
Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria

Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here, genome-wide analysis revealed that Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate development of new medicines and research tools for genome exploration.