Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of Magnetic Bead-Based Cell Selection into Complex Isolations

Magnetic bead-based analyte capture has emerged as a ubiquitous method in cell isolation, enabling the highly specific capture of target populations through simple magnetic manipulation. To date, no “one-size fits all” magnetic bead has been widely adopted leading to an overwhelming number of commercial beads. Ultimately, the ideal bead is one that not only facilitates cell isolation but also proves compatible with the widest range of downstream applications and analytic endpoints. Despite the diverse offering of sizes, coatings, and conjugation chemistries, few studies exist to benchmark the performance characteristics of different commercially available beads; importantly, these bead characteristics ultimately determine the ability of a bead to integrate into the user’s assay. In this report, we evaluate bead-based cell isolation considerations, approaches, and results across a subset of commercially available magnetic beads (Dynabeads FlowComps, Dynabeads CELLection, GE Healthcare Sera-Mag SpeedBeads streptavidin-blocked magnetic particles, Dynabeads M-270s, Dynabeads M-280s) to compare and contrast both capture-specific traits (i.e., purity, capture efficacy, and contaminant isolations) and endpoint compatibility (i.e., protein localization, fluorescence imaging, and nucleic acid extraction). We identify specific advantages and contexts of use in which distinct bead products may facilitate experimental goals and integrate into downstream applications.
Joint Action Unit localisation and intensity estimation through heatmap regression

This paper proposes a supervised learning approach to jointly perform facial Action Unit (AU) localisation and intensity estimation. Contrary to previous works that try to learn an unsupervised representation of the Action Unit regions, we propose to directly and jointly estimate all AU intensities through heatmap regression, along with the location in the face where they cause visible changes. Our approach aims to learn a pixel-wise regression function returning a score per AU, which indicates an AU intensity at a given spatial location. Heatmap regression then generates an image, or channel, per AU, in which each pixel indicates the corresponding AU intensity. To generate the ground-truth heatmaps for a target AU, the facial landmarks are first estimated, and a 2D Gaussian is drawn around the points where the AU is known to cause changes. The amplitude and size of the Gaussian is determined by the intensity of the AU. We show that using a single Hourglass network suffices to attain new state of the art results, demonstrating the effectiveness of such a simple approach. The use of heatmap regression allows learning of a shared representation between AUs without the need to rely on latent representations, as these are implicitly learned from the data. We validate the proposed approach on the BP4D dataset, showing a modest improvement on recent, complex, techniques, as well as robustness against misalignment errors. Code for testing and models will be available to download from this https URL.
Prevalence of commissural lip pits in population of central Gujarat: A hospital-based study

Background: Commissural lip pits (CLPs) fall among the rare congenital deformities recorded. CLP usually follows dominant hereditary pattern and may be associated with other congenital defects. CLP can appear as unilateral depression or bilateral depression. Objective: To assess the prevalence, age distribution, site and gender predilection of CLP in a central Gujarat population. Materials and Methods: Outdoor patients over a period of 6 months were examined for clinical evidence of CLPs. Results: A total of 14,403 patients were examined for the presence of CLP. CLP was identified in 381 patients with a prevalence of 2.65%. The occurrence of CLP was more in male patients. The maximum number of patients was in the age groups of 20–29 years. No significant statistical difference was observed in the distribution of CLP. Unilaterally distributed CLP was more common on the left side. Conclusion: Our study showed 2.65% prevalence of isolated CLPs with a male predilection. There was almost equal distribution of unilateral and bilateral CLP. In unilateral cases, the left side was affected the most. Although literature says lip pits can be an associated feature of certain syndromes, there were no syndromic patients in our study.
Late entry to HIV and AIDS care and treatment, Juba Teaching Hospital, Juba, South Sudan, 2013–2016

Late diagnosis of HIV and enrolment to care are global public health challenges. This study aimed to characterise late HIV diagnoses and initiation of treatment among patients at Juba Teaching Hospital (JTH) in South Sudan. We conducted a retrospective review of lab-confirmed HIV patients at JTH, 2013–2016. Demographic, clinical, and laboratory data were entered into and descriptive statistics were calculated using Microsoft Excel. We identified 401 patients, with mean age 33.71±4.54 years, 235 (59%) were female, 307 (77%) were late entry, 64 (16%) were lost to follow-up, and 57 (14%) died within 12 months of diagnosis. Among patients who presented late, 122 (57%) were female, and 112 (53%) were <34 years old. Among patients who died, 33 (58%) were male, and 52 (91%) had CD4 counts <350 cells/mm3 and World Health Organization (WHO) stage >2 at diagnosis. Late diagnosis of HIV infection is a significant public health problem in South Sudan, particularly for younger and female patients.
Robust Classification with Convolutional Prototype Learning

Convolutional neural networks (CNNs) have been widely used for image classification. Despite its high accuracies, CNN has been shown to be easily fooled by some adversarial examples, indicating that CNN is not robust enough for pattern classification. In this paper, we argue that the lack of robustness for CNN is caused by the softmax layer, which is a totally discriminative model and based on the assumption of closed world (i.e., with a fixed number of categories). To improve the robustness, we propose a novel learning framework called convolutional prototype learning (CPL). The advantage of using prototypes is that it can well handle the open world recognition problem and therefore improve the robustness. Under the framework of CPL, we design multiple classification criteria to train the network. Moreover, a prototype loss (PL) is proposed as a regularization to improve the intra-class compactness of the feature representation, which can be viewed as a generative model based on the Gaussian assumption of different classes. Experiments on several datasets demonstrate that CPL can achieve comparable or even better results than traditional CNN, and from the robustness perspective, CPL shows great advantages for both the rejection and incremental category learning tasks.
Renal Denervation Effects on Myocardial Fibrosis and Ventricular Arrhythmias in Rats with Ischemic Cardiomyopathy

Background/Aims: To investigate the impact of renal denervation (RDN) on myocardial fibrosis and ventricular arrhythmias (VAs) in rats with ischemic cardiomyopathy. Methods: An ischemic cardiomyopathy model was reproduced with myocardial infarction (MI) in adult Sprague–Dawley male rats. The RDN/Sham-RDN procedure was performed at 2 weeks after MI. Sham-MI and sham-RDN rats served as the control group. At 4 weeks after RDN, programmed electrical stimulation (PES) was used to induce VAs, including ventricular tachycardia and ventricular fibrillation, in all 3 groups (MI+RDN, MI, and control groups). At the end of PES, heart and kidney samples were harvested. Immunofluorescence labeling was used to investigate the distribution of connexin 43 (Cx43) in the infarcted border zone. Masson’s trichrome stain was adopted to determine the degree of cardiac fibrosis. Western blotting was performed to identify the expression of transforming growth factor beta 1 (TGF-β1), α-smooth muscle actin (α-SMA), and Cx43. An enzyme-linked immunosorbent assay (ELISA) was used to detect the serum levels of B-type natriuretic peptide (BNP) and the amino-terminal pro-peptides of type I and III collagen (PINP and PIIINP, respectively) and the expression level of renal norepinephrine. Results: Compared with the MI group, RDN significantly decreased the inducibility of VAs (MI+RDN 3/8 rats vs. MI 8/9 rats, P < 0.05; control 1/8 rats) with PES, reduced myocardial fibrosis estimated by collagen volume fraction (MI+RDN 31.10 ± 3.97% vs. MI 54.80 ± 16.39%, P < 0.001; control 4.41 ± 0.92% ), suppressed TGF-β1 (P < 0.01) and α-SMA (P < 0.001) levels, and attenuated both PINP (MI+RDN 41.44 ± 10.10 ng/mL vs. MI 95.49 ± 24.83 ng/mL, P < 0.001; control 11.90 ± 4.96 ng/mL) and PIIINP (MI+RDN 82.12 ± 30.79 ng/mL vs. MI 124.60 ± 26.64 ng/mL, P < 0.05; control 64.69 ± 23.84 ng/mL) levels. Moreover, RDN reversed the abnormal myocardial distribution of Cx43 and its reduction by MI damage (P < 0.01). Conclusions: RDN reduced myocardial fibrosis and suppressed VAs in a rat model of ischemic cardiomyopathy.
Ceramide species are elevated in human breast cancer and are associated with less aggressiveness

Sphingolipids have emerged as key regulatory molecules in cancer cell survival and death. Although important roles of sphingolipids in breast cancer progression have been reported in experimental models, their roles in human patients are yet to be revealed. The aim of this study was to investigate the ceramide levels and its biosynthesis pathways in human breast cancer patients. Breast cancer, peri-tumor and normal breast tissue samples were collected from surgical specimens from a series of 44 patients with breast cancer. The amount of sphingolipid metabolites in the tissue were determined by mass spectrometry. The Cancer Genome Atlas was used to analyze gene expression related to the sphingolipid metabolism. Ceramide levels were higher in breast cancer tissue compared to both normal and peri-tumor breast tissue. Substrates and enzymes that generate ceramide were significantly increased in all three ceramide biosynthesis pathways in cancer. Further, higher levels of ceramide in breast cancer were associated with less aggressive cancer biology presented by Ki-67 index and nuclear grade of the cancer. Interestingly, patients with higher gene expressions of enzymes in the three major ceramide synthesis pathways showed significantly worse prognosis. This is the first study to reveal the clinical relevance of ceramide metabolism in breast cancer patients. We demonstrated that ceramide levels in breast cancer tissue were significantly higher than those in normal tissue, with activation of the three ceramide biosynthesis pathways. We also identified that ceramide levels have a significant association with aggressive phenotype and its enzymes have prognostic impact on breast cancer patients.
Archaean Gold Mineralization in an Extensional Setting: The Structural History of the Kukuluma and Matandani Deposits, Geita Greenstone Belt, Tanzania

Three major gold deposits, Matandani, Kukuluma, and Area 3, host several million ouncez (Moz) of gold, along a ~5 km long, WNW trend in the E part of the Geita Greenstone Belt, NW Tanzania. The deposits are hosted in Archaean volcanoclastic sediment and intrusive diorite. The geological evolution of the deposits involved three separate stages: (1) an early stage of syn-sedimentary extensional deformation (D1) around 2715 Ma; (2) a second stage involving overprinting ductile folding (D2–4) and shearing (D5–6) events during N-S compression between 2700 and 2665 Ma, coeval with the emplacement of the Kukuluma Intrusive Complex; and (3) a final stage of extensional deformation (D7) accommodated by minor, broadly east-trending normal faults, preceded by the intrusion of felsic porphyritic dykes at ~2650 Ma. The geometry of the ore bodies at Kukuluma and Matandani is controlled by the distribution of magnetite-rich meta-ironstone, near the margins of monzonite-diorite bodies of the Kukuluma Intrusive Complex. The lithological contacts acted as redox boundaries, where high-grade mineralization was enhanced in damage zones with higher permeability, including syn-D3 hydrothermal breccia, D2–D3 fold hinges, and D6 shears. The actual mineralizing event was syn-D7, and occurred in an extensional setting that facilitated the infiltration of mineralizing fluids. Thus, whilst gold mineralization is late-tectonic, ore zone geometries are linked to older structures and lithological boundaries that formed before gold was introduced. The deformation-intrusive history of the Kukuluma and Matandani deposits is near identical to the geological history of the world-class Nyankanga and Geita Hill deposits in the central part of the Geita Greenstone Belt. This similarity suggests that the geological history of much of the greenstone belt is similar. All major gold deposits in the Geita Greenstone Belt lack close proximity to crustal-scale shear zones; they are associated with intrusive complexes and volcanics that formed in an oceanic plateau rather than subduction setting, and formed late-tectonically during an extensional phase. They are not characteristic of typical orogenic gold deposits.
Prognostic Significance of Reduction in Ki67 Index After Neoadjuvant Chemotherapy in Patients With Breast Cancer in Kerman Between 2009 And 2014

Background and objective: Breast cancer is the most common malignancy among women. The Neoadjuvant chemotherapy is the treatment of choice for non-operable tumors. The Ki67 is a proliferation marker that can be used to predict the therapeutic response to chemotherapy and the patients' prognosis. Methods: This retrospective study was carried out on 55 consecutive patients with breast cancer referred to a Training Tertiary Healthcare Center in Kerman, Iran since 2009 to 2014. After diagnostic approval, the tissue samples of patients were examined for estrogen and progesterone receptors, ki67 and HER2-neu markers by using immunohistochemical staining. Then the patients were treated with 6 cycles of Neoadjuvant chemotherapy regimens by Doxorubicin and Taxans or 4 chemotherapy cycles, containing Anthracycline and Cyclophosphamide and 4 cycles of Paclitaxel. After mastectomy, their samples were reexamined for ki67 again and classified into three groups (low: ki67<15%), medium (Ki67 = 16-30%) and high (Ki67> 30%). Results: Before chemotherapy, 54.5% of the patients had high expression of Ki67. But after chemotherapy, 52.7 of the patients had complete therapeutic response showing that the Ki67 level was reduced significantly (P=0.003). Conclusion: Before and after Neoadjuvant chemotherapy, Ki67 measurements may be used as a predictive marker of therapeutic response.
Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

Abstract Background The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear. Results We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago. Conclusions This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.
Assessing the costs and benefits of perioperative iron deficiency anemia management with ferric carboxymaltose in Germany

Background Perioperative administration of ferric carboxymaltose (FCM) was previously shown to reduce both the need for transfusions and the hospital length of stay in patients with preoperative iron deficiency anemia (IDA). In this study, we estimated the economic consequences of perioperative administration using FCM vs usual care in patients with IDA from the perspective of a German hospital using decision-analytic modeling. Materials and methods The model was populated with clinical inputs (transfusion rates, blood units transfused, hospital length of stay) from a previously reported randomized trial comparing FCM vs usual care for managing IDA patients undergoing elective abdominal surgery. We applied a hospital perspective to all costs, excluding surgery-related costs in both treatment arms. One-way sensitivity analyses were undertaken to evaluate key drivers of cost analysis. Results The average costs per case treated using FCM compared to usual care were €2,461 and €3,246, respectively, for resource expenses paid by hospital per case. This would suggest potential savings achieved with preoperative intravenous iron treatment per patient of €786 per case. A sensitivity analysis varying the key input parameters indicated the cost analysis is most sensitive to changes in the length of stay and the cost of hospitalization per day. Conclusion Perioperative administration of FCM results in cost savings to hospitals based on reduced blood transfusions and length of stay following elective abdominal surgery.
To know or not to know – parents’ attitudes to and preferences for prenatal diagnosis

Abstract Objective To highlight expectant parents’ attitudes concerning prenatal diagnosis, what the parents wish to know and what they chose not to know about their unborn baby, also in what form and to what extent they wish for prenatal diagnosis. Background: Parents have to make decisions concerning prenatal diagnosis. Screening programmes change rapidly and there is a need for parental influence on this development. Methods: An interview study with 10 women in late pregnancy and six partners. Results: The main categories ‘A time for preparation’ and ‘A lot but not everything’ included the parents’ positive attitudes towards prenatal diagnosis, especially if it could be carried out in early pregnancy and was of help for the baby, but also their negative attitudes toward information about possible future diseases that could not be prevented and towards invasive diagnosis. The parents had confidence in the caregivers’ offers of screening programmes, but described their own attitudes as changing from before pregnancy, when newly pregnant and after their ultrasound examination. The parents described themselves as partly lacking knowledge about what the existing options for prenatal diagnosis involved. Conclusions: There is a great need for competent caregivers to inform the parents-to-be about the different methods for fetal diagnosis available to them and also what information the different methods can give. Partners need to be involved in the decision-making process.
Le continent noir de la féminité : sexualité et/ou travail ? : Psychopathologie du travail

A partir de differentes situations concernant 1) des femmes exercant des metiers ou elles sont minoritaires (ingenieures, consultantes en entreprise, chirurgiennes, chercheures), 2) des femmes exercant des professions feminisees (infirmieres, travailleuses sociales, auxiliaires puericultrices), l’auteure discute des rapports entre le travail et la feminite. Etre une femme se revele, a l’analyse clinique, une difficulte supplementaire dans la recherche conjointe de la construction de l’identite et de l’accomplissement de soi.
Formulation and Characterization of Hydralazine Hydrochloride Biodegraded Microspheres for Intramuscular Administration

Objective: To prepare and characterize Albumin microspheres of hydralazine hydrochloride for the treatment of hypertension. Methods: Albumin microspheres of antihypertensive drug hydralazine hydrochloride were prepared by emulsion cross-linking method by using glutaraldehyde as cross-linking agent. Drug and polymer compatibility was determined by Fourier-Transform Infrared spectroscopy. To determine the effect of polymer concentration and amount of glutaraldehyde, formulations were characterized for their entrapment efficiency, particle size, surface morphology and release behavior. In vivo study was carried out on hypertensive wistar rats. Key findings: Maximum percentage entrapment efficiency (%EE) was found to be 68.20±1.03 %. Laser particle size analyzer confirmed mean particle size in the range of 31.7 to 39. 6μm. In vitro drug release studies showed a biphasic release pattern for all formulations with an initial burst effect followed by slow release for almost 24 hrs. Conclusion: In vivo study to determine antihypertensive effect of selected formulation strongly correlates with in vitro drug release behavior. The release behavior was significantly regulated by polymer concentration and volume of glutaraldehyde. The study revealed that hydralazine hydrochloride loaded albumin microspheres exhibited prolonged reduction of systolic and diastolic arterial pressure compared to hydralazine hydrochloride solution.
Significance and pitfalls of percutaneous endoscopic lumbar discectomy for large central lumbar disc herniation.

Background Percutaneous endoscopic lumbar discectomy (PELD) is a relatively less invasive treatment for lumbar disc herniation (LDH). The present study focused on the transforaminal approach (TFA) and investigated the significance of PELD via this approach for large central LDH. Methods LDH that did not show cerebrospinal fluid (CSF) on axial T2-weighted magnetic resonance images was defined as large central LDH. PELD via the TFA was performed in 11 patients with large central LDH. Pre- and post-operative statuses were evaluated using the modified Japanese Orthopedic Association (mJOA) and Numerical Rating Scale (NRS) scores. Results The patients' mean age was 44.1 years; there was single-level involvement, mostly at L4/5 (seven cases). The mean recovery rate of the mJOA score was 48.7%, and mean pre- and post-operative NRS scores were 7.1 and 1.5, respectively. The mean operative time was 38.1 min. Although there were no major complications, the dura was accidentally punctured at the initial operative step for discography in one case. LDH recurred in one case at 5 months after the operation, and the patient was treated by PELD via the TFA on the contralateral side. Conclusions The TFA for PELD is a safe, minimally invasive, effective treatment for large central LDH. However, the operator should pay attention to malpositioning of the flat and laterally expanded dural sac.