Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinct RBC alloantibody responses in type 1 interferon-dependent and -independent lupus mouse models

During transfusion of red blood cells (RBCs), recipients are exposed to both ABO and non-ABO ‘minor’ antigens. RBC donor units and recipient RBCs are not routinely matched for non-ABO antigens. Thus, recipients are exposed to many RBC alloantigens that can lead to RBC alloantibody production and subsequent clinically significant hemolysis. RBC alloantibodies also significantly limit the provision of compatible RBC units for recipients. Prior studies indicate that the frequency of RBC alloimmunization is increased during inflammatory responses and in patients with autoimmune diseases. Still, mechanisms contributing to alloimmune responses in patients with autoimmunity are not well understood. More than half of adult patients with systemic lupus erythematosus (SLE) produce type 1 interferons (IFNα/β) and express IFNα/β stimulated genes (ISGs). Previously, we reported that IFNα/β promote RBC alloimmune responses in the pristane mouse model, which develops a lupus-like phenotype that is dependent on IFNα/β signaling. However, it is unclear whether IFNα/β or the lupus-like phenotype induces alloimmunization in lupus models. Therefore, we tested the hypothesis that IFNα/β promotes RBC alloimmune responses in lupus by examining alloimmune responses in IFNα/β-independent (MRL-lpr) and IFNα/β-dependent (pristane) lupus models. Whereas pristane treatment significantly induced interferon-stimulated genes (ISGs), MRL-lpr mice produced significantly lower levels that were comparable to levels in untreated WT mice. Transfusion of murine RBCs that express the KEL antigen led to anti-KEL IgG production by pristane-treated WT mice. However, MRL-lpr mice produced minimal levels of anti-KEL IgG. Treatment of MRL-lpr mice with recombinant IFNα significantly enhanced alloimmunization. Collectively, results indicate that a lupus-like phenotype in pre-clinical models is not sufficient to induce RBC alloantibody production, and IFNα/β gene signatures may be responsible for RBC alloimmune responses in lupus mouse models. If these findings are extended to alternate pre-clinical models and clinical studies, patients with SLE who express an IFNα/β gene signature may have an increased risk of developing RBC alloantibodies and may benefit from more personalized transfusion protocols.
Contribution to the seismotectonics of Eastern Turkey from moderate and small size events

Source properties of small‐to‐moderate magnitude events in eastern Turkey were studied using high quality waveform data produced by the Eastern Turkey Seismic Experiment (ETSE). A data set of fault plane solutions was obtained for 134 earthquakes using the regional moment tensor inversion technique for 34 events with magnitude 3.7 and above, and first motion analysis for 115 earthquakes with magnitude 3.0 and higher (for 15 events both techniques were used). Most of the events studied had strike slip mechanisms in agreement with nearby local fault structures. Reverse mechanisms were more scarce and were restricted to certain areas, such as in the eastern Anatolian plateau and southwest of the Karliova junction along the Arabian plate boundary. Our results indicate a difference in the deformational style east and west of the Karliova junction which results in internal deformation in the east and westward extrusion of the Anatolian plate with no or very little internal deformation in the west. Our results also suggest that in eastern Turkey, most of the collision is taken up by strike slip faults of varying types and sizes, suggesting that the northward convergence of Arabia is being accommodated by escape tectonics. Compressive features, such as thrust faulting, which were obviously the primary faulting during the earliest stages of continental collision, are still active but are of lesser importance.
Cross Flow Microfiltration System in Separating Fermented Nixtamal Corn for Preparation of Natural Folic Acid

A purification process of biomass of nixtamal yellow corn fermented by Rhizopus oligosporus strain C1 (FNC-A) and Rhizopus sp (FNC-B) was performed using a microfiltration (MF) membrane with pore size 0.15 Âµm installed in a crossflow microfiltration (CFMF) system to obtain retentate and permeate fractions as natural folic acid preparations. CFMF process was conducted at room temperature with a pump motor frequency (PMF) of 10 Hz (flow rate of 3.5 L/min) and a transmembrane pressure (TMP) of 4 bar for 0, 15, 30, 45, 60, 75, and 90 minutes. Based on optimum folic acid, the results showed that the best treatments of FNC-B and FNC-B were achieved at 90 min, resulting in a folic acid increase in retentate of FNC-A and FNC- B of 72.61 and 95.26%, reducing sugar of 20.41 and 170.93% (1.7-folds), total sugars of 155.51% (1.55-folds) and 426.76% (4.27-folds), and dissolved protein of 55.33 and 39.20%, and decrease in total solids of 88.91 and 91.64%, respectively, compared to initial biomass of FNC-A and FNC-B. The MFCF system effectively separated folic acid in retentates of FNC-A (33.77%) and FNC-B (95.27%) at the optimal condition. Folic acid monomers predominated the characteristics of FNC-A and FNC-B in optimum conditions with molecular weights of 442.10 and 442.18 Dalton, the average particle size of 38.31 Î¼m and 37.97 Î¼m, and distribution of particles at 10, 50, and 90% from the particle size 10.31, 26.32 and 81.55 Î¼m, and 10.37, 28.04 and 76.09 Î¼m, respectively.
Design, fabrication and performance evaluation of centrifugal sunflower dehuller for small-scale enterprises in developing countries

Sunflower is grown by small-scale farmers in many developing countries like Tanzania. Lack of effective machines for dehulling sunflower seeds has resulted in high oil losses during extraction, especially for small- and medium-scale enterprise. This paper reports on the design, fabrication and performance evaluation (in terms of throughput capacity, dehulling efficiency and kernel breakage efficiency) of a centrifugal machine for dehulling sunflower seeds. The purpose was to improve the dehulling efficiency and to reduce kernel breakage of the dehulled seeds. The machine consists of a frame, feeding hopper, power shaft, bearings system, dehulling chamber and power unit. The results showed that the higher the impeller speed, the higher the throughput capacity and dehulling efficiency. The highest dehulling efficiency was 94.3% which is significantly higher than that of existing abrasive dehullers (17%). However, high speed also resulted in increased kernel breakage (5−20.9%) hence reducing the quality of the dehulled seeds. Thus an impeller speed of 1445 rpm was selected for the operation of the machine. The results suggest that the designed centrifugal dehuller can be used by small- and medium-scale sunflower oil enterprises for improving oil extraction.
DNA Vaccines: Their Formulations, Engineering and Delivery

The concept of DNA vaccination was introduced in the early 1990s. Since then, advancements in the augmentation of the immunogenicity of DNA vaccines have brought this technology to the market, especially in veterinary medicine, to prevent many diseases. Along with the successful COVID mRNA vaccines, the first DNA vaccine for human use, the Indian ZyCovD vaccine against SARS-CoV-2, was approved in 2021. In the current review, we first give an overview of the DNA vaccine focusing on the science, including adjuvants and delivery methods. We then cover some of the emerging science in the field of DNA vaccines, notably efforts to optimize delivery systems, better engineer delivery apparatuses, identify optimal delivery sites, personalize cancer immunotherapy through DNA vaccination, enhance adjuvant science through gene adjuvants, enhance off-target and heritable immunity through epigenetic modification, and predict epitopes with bioinformatic approaches. We also discuss the major limitations of DNA vaccines and we aim to address many theoretical concerns.
Methylenetetrahydrofolate reductase polymorphic variants C677T and A1298C in rectal cancer in Slavic population: significance for cancer risk and response to chemoradiotherapy

Background: Methylenetetrahydrofolate reductase (MTHFR) single nucleotide polymorphisms (SNPs) have been suggested as risk, prognostic, and predictive factors for colorectal cancer in various populations, but have not been validated so far. The aim of this study was to examine the association of MTHFR C677T (rs1801133) and A1298C (rs1801131) single nucleotide polymorphisms with the risk of rectal cancer as well as the response to neoadjuvant chemoradiotherapy (nCRT) based on 5-Fluorouracil (5-FU)/leucovorin (LV) in the locally advanced setting. Patients and methods: This case-control study included 119 healthy controls and 97 patients with locally advanced rectal cancer (LARC). For MTHFR genotyping, restriction fragment length polymorphism analysis (PCR-RFLP) was employed. Results: In silico analysis highlighted that SNPs C677T and A1298T correlate with MTHFR gene expression, and that gene expression profile correlates with cancer risk and stage. Using dominant and recessive models, it was found that the MTHFR 677CC vs. 677CT+677TT have increased risk of cancer development (odds ratio (OR): 2.27; 95% confidence interval (CI): 1.30–3.95, p = 0.002) as well as 677CC+677CT compared to 677TT (OR: 4.18, 95% CI: 1.16–14.99, p = 0.014). MTHFR 1298AA also shown increased risk for cancer development compared to 1298AC+1298CC (OR:2.0, 95% CI: 1.20–3.59, p = 0.035) Statistical analysis of combined genotypes highlighted the protective role of CT/AC combined genotype (OR: 3.15 95% CI: 1.576–6.279, p = 0.002) while the CC/AA genotype showed an increased risk for rectal cancer development (OR: 2.499, 95% CI: 1.246–5.081, p = 0.016) The carriers of the 677C/1298A haplotype had the highest risk for developing rectal cancer (OR: 1.74; 95% CI: 1.198–2.530, p = 0.002) while the 677T/1298C haplotype seems to provide a protective effect. (OR: 0.44; 95%CI 0.248–0.795, p = 0.003). No significant association with response to chemoradiotherapy was found. Conclusion: Our data point to MTHFR 667C allele and 1298A alleles as low-penetrance risk factors for rectal cancer in our population. To the best of our knowledge, this is the first study of this type performed on the Slavic population in the Western Balkan, as various population-based factors might also be significant our findings can be used for future meta-analyses and the construction of genetic cancer risk prediction panels.
The Effect of Vitamin D Supplementation on Size of Uterine Leiomyoma in Women with Vitamin D Deficiency

BACKGROUND: Uterine leiomyomas (fibroids) are the most common benign genital tumors in women. There is a high prevalence of vitamin D deficiency and uterine leiomyomas. AIM: To evaluate the effect of vitamin D supplementation on the size of uterine leiomyoma in women with vitamin D deficiency. MATERIALS AND METHODS: It is case–control prospective study which was done in Gynecology Ward at Basrah Maternity and Child Hospital from January 2020 to August 2022. Patients at ages 20–45 years were initially included in the study if they were diagnosed with 1–3 uterine fibroids with a mean diameter ≥10 mm. Serum vitamin D levels were estimated for all women before intervention and in those with deficiency of vitamin D (level <30 ng/mL). Patients with vitamin D deficiency were divided into 2 groups. The 1st group was women who received vitamin D 50,000 cholecalciferol (oral solution) IU weekly for 10 weeks followed by 2000 IU daily for 6–9 month (as study group), while 2nd group received placebo (control group). After the duration of treatment, vitamin D level was estimated and sonography was done to assess the fibroid size at 9–12 months later. In relation to the achievement of normal 25-OH-D3 levels, after the supplementation, the studied population were divided into 2 subgroup of patients: “gave response” and “non-responders” according to their response to treatment. RESULTS: Vitamin D level was 17.6 (±3.0) ng/mL and calcium status was 7 mg/dL among 43 females of the study group. Vitamin D level was 34.7 ± 5 ng/mL after 12 months vitamin treatment (p < 0.05). The early vitamin level among 23 control females was 22.4 ± 7.8 ng/mL in comparison to 24.6 ± 6.7 ng/mL after 12 months (p > 0.05). There was no change for calcium level before and after 12 months period (8.6 vs. 7.9 mg/dL respectively). No changes were noticed among both the study and the control groups as far as the type and position of leiomyoma between the 1st and the 2nd ultrasound after 12 months of therapy. CONCLUSION: Lower serum vitamin D levels are significantly associated with the occurrence of uterine fibroids.
Modeling the interaction between presalt seamounts and gravitational failure in salt-bearing passive margins: The Messinian case in the northwestern Mediterranean Basin

AbstractThe northwest Mediterranean Basin includes a thick Messinian salt sequence composed of three evaporitic units. From these, the intermediate unit, which is dominantly composed of halite, acted as a gravitational detachment favoring the downslope failure of the overlying sediments in a thin-skinned deformation regime. As a result, the structure of the margin is characterized by an upper extensional domain with basinward-dipping listric normal faults and a lower contractional domain that accommodates upslope extension by folding, salt inflation, or diapir squeezing. Lower to middle Miocene volcanic seamounts (presalt reliefs) located at the upper extensional domain locally disrupted the evaporitic units and produced salt flow perturbations. They acted as passive buttresses during the gravitational failure modifying the structural zonation of the margin. Using an experimental approach (sandbox models), we analyze the role played by seamounts during the kinematic evolution of passive margins and how th.
Nutrient sensing in the alimentary tract

2 ACKNOWLEDGEMENTS . 4 TABLE OF CONTENTS . 6 LIST OF FIGURES . 10 LIST OF TABLES . 14 LIST OF ABBREVIATIONS . 15 CHAPTER 1 . 17 GENERAL INTRODUCTION . 17 1 GENERAL INTRODUCTION . 18 1.1 Metabolic syndrome & the modern diet . 18 1.2 Metabolism & the gut-brain axis . 23 1.2.1 Gut peptides . 23 1.2.2 Nutrient sensing in the alimentary tract . 25 1.3 Expression of sugar transporters and sensors in the alimentary tract . 30 1.3.1 Expression of sugar transporters in the gastrointestinal tract . 30 1.3.2 Expression of the sweet-taste machinery in the alimentary tract . 31 1.3.3 Expression of the novel sugar sensor SGLT3 in the alimentary tract . 34 1.4 Nutrient sensor mechanisms as targets for metabolic syndrome . 38 1.5 Aims, hypotheses & rationale . 40 CHAPTER 2 . 42 SHORT-TERM REGULATION OF SUGAR TRANSPORT IN AN IN VITRO MODEL OF ENTEROCYTES — CACO-2/TC7 CELLS . 42 2 SHORT-TERM REGULATION OF SUGAR TRANSPORT IN AN IN VITRO MODEL OF ENTEROCYTES — CACO-2/TC7 CELLS . 43 2.1 Summary . 43 2.2 Background . 45 2.3 Chapter Overview – Short-term regulation of sugar transport in vitro . 51 2.4 Materials & Methods . 52 7 2.4. 1 Cell culture . 52 2.4. 2 Radio-labelled sugar-uptake assay . 52 2.4. 3 RNA isolation . 53 2.4. 4 Reverse Transcription Polymerase Chain Reaction (RT-PCR) . 54 2.4. 5 Agarose gel electrophoresis . 55 2.4. 6 Statistics . 56 2.5 Results . 57 2.5. 1 D-Glu & Fru uptake is carrier-mediated and linear in Caco-2/TC7 cells . 57 2.5. 2 D-Glu transport is regulated by D-Glu in Caco-2/TC7 cells . 58 2.5. 3 Dissection of transporters responsible for higher D-Glu transport . 59 2.5. 4 The sweet-taste receptor T1R2/3 does not regulate sugar transport in Caco-2/TC7 cells . 62 2.5. 5 HFCS, but not sucrose or fructose, stimulates sugar transport in Caco-2/TC7 cells . 64 2.6 Discussion . 67 2.7 Limitations of the study . 70 2.8 Conclusion . 72 CHAPTER 3 . 73 DIURNAL REGULATION OF NUTRIENT SENSORS ALONG THE ALIMENTARY TRACT . 73 3 DIURNAL REGULATION OF NUTRIENT SENSORS ALONG THE ALIMENTARY TRACT . 74 3.1 Summary . 74 3.2 Background . 76 3.2.1 Circadian clock . 76 3.2.2 Circadian clock and metabolic disease . 78 3.3 Chapter Overview – Diurnal expression of nutrient sensors along the alimentary tract . 81 3.4 Materials & Methods . 82 3.4. 1 Animal ex vivo studies . 82 3.4. 2 RNA extraction. 82 3.4. 3 Microarray analysis . 83 3.4. 4 Reverse Transcription Polymerase Chain Reaction (RT-PCR) . 83 3.4. 5 Real-time PCR . 84 3.4. 6 QuantiFast® tas1r2 & tas1r3 real-time PCR . 85 3.4. 7 Protein extraction. 85 3.4. 8 Bicinchoninic acid (BCA) assay . 85 3.4. 9 Western blotting . 86 3.4. 10 In silico promotor analysis . 87 3.4. 11 Statistics . 88 3.5 Results . 89 3.5. 1 Diurnal rhythm of sugar transporters in the gastrointestinal tract . 89 3.5. 2 Diurnal rhythms of taste sensors in the gastrointestinal tract . 92 3.5. 3 Diurnal rhythms of gut peptides in the gastrointestinal tract . 96
How Highly Stressed Brittle Rock Failure Impacts Tunnel Design

This lecture focuses on brittle rock and rock mass failure modes to illustrate how highly stressed rock behaviour near deep excavations differs from rock far from an excavation, i.e., it fails predominantly by spalling rather than by shear. As a consequence, the often adopted shear failure models do not represent spalling-type failure processes and thus are often inadequate for the design of tunnels and their support systems. It is also discussed how swelling rock problems in tunnelling might be related to brittle failure processes and how a change to more appropriate modelling approaches might assist in understanding and controlling swelling. Recent developments and implications of practical importance are highlighted, particularly with respect to the selection of strength parameters for support design of underground excavations in highly stressed rock. Several case examples are used to highlight how a better understanding of the spalling behaviour may help to prevent costly delays and rehabilitation work. (2) Risk management based on the most critical behaviour modes: As well illustrated by Hoek (1992), to manage uncertainty, it is necessary to compare capacities and demands and to gradually narrow the distributions from pre-feasibility studies to final designs, and to manage any remnant uncertainties by an observational engineering approach utilizing monitoring as the basis for refinement (Figure 1). 0.00 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0 50 100 150 200 D en si ty (C ap ac ity a nd D em an d) Design parameter fD(X); CoV =30%
Laboratory investigation on hydraulic anisotropy behavior of unsaturated soil

Hydraulic anisotropy behavior of unsaturated soil has not been fully investigated. Direct laboratory measurement and indirect determination of hydraulic anisotropy under a drying condition were carried out on statically compacted specimens having different initial conditions. Direct measurement of permeability was carried out using an unsaturated triaxial permeameter whereas indirect determination of permeability was performed through statistical estimation via a measured drying soil–water characteristic curve (SWCC). In this research, two orientations — specifically horizontal-layering (HL) and vertical-layering (VL) orientations — were prepared for a given specimen from statically compacted homogeneous sand–kaolin. The results from both direct measurement and indirect determination of hydraulic anisotropy were in good agreement. Hydraulic anisotropy under an unsaturated condition was found to be similar with that in a saturated condition. Moreover, hydraulic anisotropy was reflected in the ratio of tran.
Probing Disk Ice Content and Polycyclic Aromatic Hydrocarbon Emission through Multiband MagAO+Clio Images of HD 141569

We present resolved images of the inner disk component around HD 141569A using the Magellan adaptive optics system with the Clio2 1–5 μm camera, offering a glimpse of a complex system thought to be in a short evolutionary phase between protoplanetary and debris disk stages. We use a reference star along with the Karhunen–Loéve image projection (KLIP) algorithm for point-spread function subtraction to detect the disk inward to about 0. ″24 (∼25 au assuming a distance of 111 pc) at high signal-to-noise ratios at L′ (3.8 μm), Ls (3.3 μm), and narrowband Ice (3.1 μm). We identify an arc or spiral arm structure at the southeast extremity, consistent with previous studies. We implement forward modeling with a simple disk model within the framework of a Markov Chain Monte Carlo sampler to better constrain the geometrical attributes and photometry using our KLIP-reduced disk images. We then leverage these modeling results to facilitate a comparison of the measured brightness in each passband to find a reduction in scattered light from the disk in the Ice filter, implying significant absorption due to water ice in the dust. Additionally, our best-fit disk models exhibit peak brightness in the southwestern, back-scattering region of the disk, which we suggest to be possible evidence of 3.3 μm polycyclic aromatic hydrocarbon emission. However, we point out the need for additional observations with bluer filters and more complex modeling to confirm these hypotheses.
Diurnal Ejection of Boulder Clusters on Comet 67P Lasting beyond 3 au

Ejection of large boulder-like debris is a vigorous form of cometary activity that is unlikely induced by water ice out-gassing alone but rather associated with the sublimation of super-volatile ices. Though perceived on several comets, the actual pattern and mechanism of such activity are still unclear. Here we report on a specialized observation of ejections of decimeter- to meter-sized boulders on comet 67P/Churyumov-Gerasimenko outbound between 2.5 and 3.3 au from the Sun. With a common source region, these events recurred in local morning. The boulders of elongated shapes were ejected in clusters at low inclinations comparable to the solar elevation below 40° at the time. We show that these chunks could be propelled by the surrounding asymmetric gas field that produced a distinct lateral acceleration. Possibly both water and carbon dioxide have contributed to their mobilization, while the season and local topography are among deciding factors. The mechanisms for sustaining regular activity of comets at large heliocentric distances are likely more diverse and intricate than previously thought.
DR-GPT: a large language model for medical report analysis of diabetic retinopathy patients

Diabetic retinopathy (DR) is a sight-threatening condition caused by diabetes. Screening programmes for DR include eye examinations, where the patient's fundi are photographed, and the findings, including DR severity, are recorded in the medical report. However, statistical analyses based on DR severity require structured labels that calls for laborious manual annotation process if the report format is unstructured. In this work, we propose a large language model DR-GPT for classification of the DR severity from unstructured medical reports. On a clinical set of medical reports, DR-GPT reaches 0.975 quadratic weighted Cohen's kappa using truncated Early Treatment Diabetic Retinopathy Study scale. When DR-GPT annotations for unlabeled data are paired with corresponding fundus images, the additional data improves image classifier performance with statistical significance. Our analysis shows that large language models can be applied for unstructured medical report databases to classify diabetic retinopathy with a variety of applications.