gebhart/patrepeval huggingface dataset:
Chromatin‐Remodeling Factors Allow Differentiation of Bone Marrow Cells into Insulin‐Producing Cells (2006)

Type 1 diabetes is caused by the destruction of pancreatic beta-cells by T cells of the immune system. Islet transplantation is a promising therapy for diabetes mellitus. Bone marrow stem cells (BMSC) have the capacity to differentiate into various cell lineages including endocrine cells of the pancreas. To investigate the conditions that allow BMSC to differentiate into insulin-producing cells, a novel in vitro method was developed by using the histone deacetylase inhibitor, trichostatin A (TSA). BMSC, cultured in presence of TSA, differentiated into islet-like clusters under appropriate culture conditions. These islet-like clusters were similar to the cells of the islets of the pancreas. The islet-like clusters showed endocrine gene expression typical for pancreatic beta-cell development and function, such as insulin (I and II), glucagon, somatostatin, GLUT-2, pancreatic duodenal homeobox-1 (PDX-1), and Pax 4. Immunocytochemistry confirmed islet-like clusters contained pancreatic hormones. The colocalization of insulin and C-peptide was also observed. Enzyme-linked immunosorbent assay analysis demonstrated that insulin secretion was regulated by glucose. Western blot analysis demonstrated the presence of stored insulin. Electron microscopy of the islet-like cells revealed an ultrastructure similar to that of pancreatic beta-cells, which contain insulin granules within secretory vesicles. These findings suggest that histone-deacetylating agents could allow the differentiation of BMSC into insulin-producing beta-cells.
Does Lumbar Spinal Fusion Affect THA Stability – An Evaluation of Surgical Approach for THA? (2020)

Introduction: Lumbar spine fusion (LSF) has been demonstrated to increase the risk of dislocation in patients who have undergone Total Hip Arthroplasty (THA), especially when the LSF was performed prior to the THA. Rates of dislocation have been published as high as 7.4%. The intrinsic stability of THA is higher after anterior surgical approaches as compared to a posterior approach for THA – possibly related to retention of the posterior capsule with anterior approaches to the hip. There are no data on whether surgical approach for THA – anterior vs posterior – affects this increased risk of dislocation in patients with LSF. The purpose of this project is to determine whether anterior or posterior THA approach type influences the rate of dislocation in patients who have a concomitant lumbar spinal fusion.\nMethods: Patients who had received both an LSF and a THA were identified and placed into one of two groups: anterior or posterior THA approach. Pearson Chi-square analysis or Fisher’s Exact Test was conducted to compare the differences in dislocation rates between groups. A subsequent analysis was conducted, stratifying patients based on the order in which they received the LSF or THA—with a focus on the LSF prior to THA subgroup.\nResults: A total of 690 (92.1%) patients were in the anterior group, while the remaining 59 (7.9%) were in the posterior THA approach group. There was a total of 3 dislocations (0.4%) and 2 dislocations (3.4%) after a posterior hip arthroplasty. This represents a 9-fold higher frequency of dislocation using a posterior approach (p=0.052). When stratifying groups based on the order of LSF or THA received, a total of 412 patients (55.0%) received an LSF prior to THA, with 376 (91.3%) patients in the anterior approach group and the remaining 36 (8.7%) in the posterior THA group. There was 1 dislocation (0.3%) in the anterior THA group and 2 dislocations (5.6%) in the posterior THA group. The 19-fold difference in dislocation rates between approach types in this subgroup was found to be significant (0.021).\nDiscussion: The anterior approach appears to provide substantial stability to the THA construct when compared to the posterior approach—this is maintained even in the presence of a prior lumbar spinal fusion. This is a particularly important finding that suggests surgeons may want to consider opting to perform an anterior THA in patients who have also had a previous LSF.
Calcul des Fréquences de Phonons dans les Cristaux Moléculaires a Partir des Potentiels d'Intéraction Atomiques I. Possibilitiés de Réorientation des Molécules de Benzène et d'Hexaméthylbenzène dans Leur Réseau Cristallin (1973)

Abstract Calculations of reorientation barrier heights and phonon frequencies in molecular crystals have been carried out, using interaction potential between nonbonded atoms, in the frame of the rigid-body approximation. Results obtained with various interaction parameters, unit cell parameters and molecular models are compared with available experimental data from RMN, IR and Raman spectra of crystalline benzene. Results obtained for hexamethylbenzene are also compared with experimental data.
Diarrhea in Lambs Experimentally Infected with Cryptosporidium Isolated from Calves (1981)

Two to 5 days after oral inoculation with Cryptosporidium obtained from infected calves, 7 newborn specific-pathogen-free lambs became depressed and anorectic and developed diarrhea. Four moribund lambs were killed within 3 days after onset of illness, and the 3 other lambs died after protracted intermittent diarrhea and reduced milk intake, which lasted up to 14 days. The small and large intestines were heavily infected with Cryptosporidium, with the terminal portion of the ileum being the most severely affected. Histologic examination revealed villous atrophy, with considerable fusion and epithelial cross-bridging between villi. Lambs infected at 5 to 20 days of age had less severe clinical signs of disease, with intermittent diarrhea, reduced milk intake, and growth retardation. Lambs infected at 30 days of age became infected with the organism, but did not develop clinical signs of disease or growth retardation.
The hypotransferrinaemic mouse: Ultrastructural and laser microprobe analysis observations (1995)

Homozygote hypotransferrinaemic mice (hpx/hpx) have cytopathological features similar to those of human congenital atransferrinaemia, genetic haemochromatosis, and neonatal haemochromatosis. These conditions all have in common high levels of cytotoxic non-transferrin-bound serum iron. This study describes the ultrastructural features of iron overload in liver, pancreas, heart, and small intestine of 2- and 12-month-old hypotransferrinaemic mice. Electron microscopic studies of unstained sections showed early parenchymal cell siderosis, with accumulation of numerous ferritin particles and clusters in the cytosol, as well as ferritin and haemosiderin in lysosomes (siderosomes). In the 12-month-old animals, iron was also found in Kupffer cells and macrophages in other tissues. In addition, there were conspicuous iron-containing compounds in the bile canaliculi, and marked iron deposition in the pancreas and heart. Laser microprobe mass analysis (LAMMA) enabled localization and relative quantitation of iron deposition in subcellular compartments providing in situ documentation of iron accumulation in siderosomes and contributed in assessing total cytosolic iron in various cell types. Moreover, it demonstrated the importance and magnitude of the biliary route for iron excretion in these animals.
MURI: Surface-Templated Bio-Inspired Synthesis and Fabrication of Functional Materials (2006)

Abstract : The use of biosynthons and bio-inspired assembly is a new, but extremely powerful approach to the synthesis of designer materials. The development of new methods for patterning biological molecules on the nanometer to micron length scale will lead to new biomaterials that can be used for fabricating a variety of nanostructured organic and inorganic materials that are of vital importance to the Department of Defense. These include catalytic peptide tubes, host-guest materials for molecular separations, quantum dot and magnetic particle arrays, bio-nanocircuitry, photonic bandgap and 3-D power structures, and novel bio-warfare detection materials. This grant has pursued an integrated research effort that has focused on 3 thematic areas of research: (1) biocompatible nanolithography methods for patterning and templating of 2-D and 3-D nanostructured materials; (2) nucleic acid-based approaches to preparing extended functional architectures both in solution and from predesigned, nanostructured surface templates, and (3) protein-based or inspired architectures. The highlights of our accomplishments are featured in the following report.
EMT in Breast Carcinoma—A Review (2016)

The epithelial to mesenchymal transition (EMT) is a cellular program that is involved in embryonic development; wound healing, but also in tumorigenesis. Breast carcinoma (BC) is the most common cancer in women worldwide, and the majority of deaths (90%) are caused by invasion and metastasis. The EMT plays an important role in invasion and subsequent metastasis. Several distinct biological events integrate a cascade that leads not only to a change from an epithelial to mesenchymal phenotype, but allows for detachment, migration, invasion and ultimately, colonization of a second site. Understanding the biological intricacies of the EMT may provide important insights that lead to the development of therapeutic targets in pre-invasive and invasive breast cancer, and could be used as biomarkers identifying tumor subsets with greater chances of recurrence, metastasis and therapeutic resistance leading to death.
Compton Scattering by Internal Shields Based on Melanin-Containing Mushrooms Provides Protection of Gastrointestinal Tract from Ionizing Radiation (2012)

There is a need for radioprotectors that protect normal tissues from ionizing radiation in patients receiving high doses of radiation and during nuclear emergencies. We investigated the possibility of creating an efficient oral radioprotector based on the natural pigment melanin that would act as an internal shield and protect the tissues via Compton scattering followed by free radical scavenging. CD-1 mice were fed melanin-containing black edible mushrooms Auricularia auricila-judae before 9 Gy total body irradiation. The location of the mushrooms in the body before irradiation was determined by in vivo fluorescent imaging. Black mushrooms protected 80% of mice from the lethal dose, while control mice or those given melanin-devoid mushrooms died from gastrointestinal syndrome. The crypts of mice given black mushrooms showed less apoptosis and more cell division than those in control mice, and their white blood cell and platelet counts were restored at 45 days to preradiation levels. The role of melanin in radioprotection was proven by the fact that mice given white mushrooms supplemented with melanin survived at the same rate as mice given black mushrooms. The ability of melanin-containing mushrooms to provide remarkable protection against radiation suggests that they could be developed into oral radioprotectors.
A new generic method for semi-automatic extraction of river and road networks in low- and mid-resolution satellite images (2010)

This paper addresses the problem of semi-automatic extraction of road or hydrographic networks in satellite images. For that purpose, we propose an approach combining concepts arising from mathematical morphology and hydrology. The method exploits both geometrical and topological characteristics of rivers/roads and their tributaries in order to reconstruct the complete networks. It assumes that the images satisfy the following two general assumptions, which are the minimum conditions for a road/river network to be identifiable and are usually verified in low- to mid-resolution satellite images: (i) visual constraint: most pixels composing the network have similar spectral signature that is distinguishable from most of the surrounding areas; (ii) geometric constraint: a line is a region that is relatively long and narrow, compared with other objects in the image. While this approach fully exploits local (roads/rivers are modeled as elongated regions with a smooth spectral signature in the image and a maximum width) and global (they are structured like a tree) characteristics of the networks, further directional information about the image structures is incorporated. Namely, an appropriate anisotropic metric is designed by using both the characteristic features of the target network and the eigen-decomposition of the gradient structure tensor of the image. Following, the geodesic propagation from a given network seed with this metric is combined with hydrological operators for overland flow simulation to extract the paths which contain most line evidence and identify them with the target network.
Urine Dipstick Analysis on Automated Platforms: Is a Reliable Screening Tool for Proteinuria? An Experience from Umberto I Hospital in Rome (2023)

Urinalysis is commonly used as a screening tool for kidney disease. In many cases, the dipstick urine assay includes the assessment of albumin/protein and creatinine; consequently, the value of their ratio is available on the urine section report. Identification of albuminuria/proteinuria at early stages is an important issue to prevent or at least delay the onset of chronic kidney disease (CKD), kidney failure, and the progression of cardiovascular damage linked to the kidney's loss of function. Sensitive and specific diagnostic methods are required for the assessment of such an important biomarker: urine albumin, creatinine, and their ratio (ACR) measured with quantitative assays are considered the gold standard. Routine dipstick methods (more rapid and at a lower cost) are intended for wide population screening. The aim of our study was to verify the reliability of an automated urinalysis dipstick method by comparing the results with the quantitative test of creatinine and albumin performed on a clinical chemistry platform. The first-morning voids of 249 patients who arrived from different departments were analyzed in the Central Laboratory of the University Hospital Policlinico Umberto I in Rome. We found a good correlation between the two assays, even though we observed that the dipstick assessment tends to overestimate the ACR's value, disclosing a higher number of false positives if compared to the reference method. As an important novelty in this study, we analyzed our data considering age (starting from pediatric to geriatric patients) and sex as variables for a sub-stratification of the participants. Our results show that positive values need to be confirmed with quantitative methods, especially in women and younger people, and that from samples that resulted as diluted at the dipstick assay, the ACR's values can be obtained if they are reanalyzed with quantitative assays. Moreover, patients with microalbuminuria (ACR 30-300 mg/g) or severe albumin urinary excretion (ACR > 300 mg/g) should be reanalyzed using quantitative methods to obtain a more reliable calculation of the ACR.
SVM-based Video Segmentation and Annotation of Lectures and Conferences (2014)

This paper presents a classification system for video lectures and conferences based on Support Vector Machines (SVM). The aim is to classify videos into four different classes (talk, presentation, blackboard, mix). On top of this, the system further analyses presentation segments to detect slide transitions, animations and dynamic content such as video inside the presentation. The developed approach uses various colour and facial features from two different datasets of several hundred hours of video to train an SVM classifier. The system performs the classification on frame-by-frame basis and does not require pre-computed shotcut information. To avoid over-segmentation and to take advantage of the temporal correlation of succeeding frames, the results are merged every 50 frames into a single class. The presented results prove the robustness and accuracy of the algorithm. Given the generality of the approach, the system can be easily adapted to other lecture datasets.
CDVS feature selection on embedded systems (2015)

Mobile image retrieval and pairwise matching applications pose a unique set of challenges. As communicating large amount of data could take tens of seconds over a slow wireless link, MPEG defined the CDVS standard to transfer over the network only the data essential to the matching, and not the entire image. However, the extraction of salient image features is a very time consuming process, and it may still require times in the order of seconds when running on CPU of modern mobile devices. To reduce feature extraction computation times, we re-design the MPEG-CDVS feature selection algorithm for highly parallel embedded GPUs. We consider two different approaches compliant to the standard. In the first one, feature selection is performed before the orientation assignment stage. In the second one, it is performed after. We present a complete experimental analysis on a large test set. Our experiments show that our GPU-based approaches are remarkably faster than the CPU-based reference implementation of the standard, while maintaining a comparable precision in terms of true and false positive rates. To sum up, our solutions have been proved to be effective for real-time applications running on modern embedded systems.
CCR5 Antagonists:  3-(Pyrrolidin-1-yl)propionic Acid Analogues with Potent Anti-HIV Activity (2003)

[reaction: see text] A novel approach to alpha,alpha-disubstituted-beta-amino acids (beta(2,2)-amino acids) was employed in the synthesis of a series of 3-(pyrrolidin-1-yl)propionic acids possessing high affinity for the CCR5 receptor and potent anti-HIV activity. The rat pharmacokinetics for these new analogues featured higher bioavailabilities and lower rates of clearance as compared to cyclopentane 1.
Radioimmunoassay for the Detection of the Core of the Dane Particle and Antibody to It (1973)

A radioimmunoassay for detecting the core of the Dane particle and antibody to it was developed. The core was detected in concentrates of Dane particles but not in preparations of purified 22-nm forms of hepatitis B antigen. Detergent treatment of Dane particles increased the detectability of the core. Antibody to the core appeared following acute type B hepatitis infection and could be consistently demonstrated in chronic carriers of hepatitis B antigen. Such antibody was found less frequently in patients with evidence of re-exposure to hepatitis B antigen; it could not be detected in pooled hepatitis B immune serum globulin.
Real-time deblurring of handshake blurred images on smartphones (2015)

This paper discusses an Android app for the purpose of removing blur that is introduced as a result of handshakes when taking images via a smartphone. This algorithm utilizes two images to achieve deblurring in a computationally efficient manner without suffering from artifacts associated with deconvolution deblurring algorithms. The first image is the normal or auto-exposure image and the second image is a short-exposure image that is automatically captured immediately before or after the auto-exposure image is taken. A low rank approximation image is obtained by applying singular value decomposition to the auto-exposure image which may appear blurred due to handshakes. This approximation image does not suffer from blurring while incorporating the image brightness and contrast information. The eigenvalues extracted from the low rank approximation image are then combined with those from the shortexposure image. It is shown that this deblurring app is computationally more efficient than the adaptive tonal correction algorithm which was previously developed for the same purpose.
Type 1 diabetes mellitus and oral health: assessment of coronal and root caries (2001)

Factors associated with presence of coronal and root caries and fillings are discussed. Possible causes and implications for the association between DFS and diabetic nephropathy are provided.
A BLEOMYCIN-INACTIVATING ENZYME IN MOUSE LIVER (1974)

Affinity chromatography of a bleomycin-inactivating enzyme was studied on Sepharose 4 B-bleomycin A5 and Sepharose 4 B-lysinamide. Mouse liver was homogenized, and the enzyme extracted by ammonium sulfate precipitation and Sephadex G-200 chromatography. Affinity chromatography of the extract on Sepharose 4 B-lysinamide gave 25-fold purified enzyme, Further purification vas not successful because of instability of the enzyme. It hydrolyzed L-lysinamide, L-lysyl-β-naphthyl-amide, L-arginy1-β-naphthylamide, L-lysyl-L-lysine and Iysyl-bradykinin, but not leucinamide or L-leucyl-β-naphthylamide. Hydrolysis of L-lysyl-β-naphthylamide and L-arginyl-β-naphthylamide by the enzyme was competitively inhibited by bleomycin B2. The bleomycin-inactivating enzyme of rat liver was separated from a known aminopeptidase B.
A 2-Step Approach to Myeloablative Haploidentical Stem Cell Transplantation with Optimized T-Cell Dosing: Early Immune Reconstitution Leads to Better Outcomes (2013)

We developed a 2-step approach to myeloablative haploidentical HSCT in which patients receive a large fixed dose of cyclophosphamide (CY)-tolerized T cells separately frm the HSC infusion in the hopes of accelerating post HSCT immune reconstitution (IR). The uniformity of the T cell dosing facilitates comparison of patients without (low risk) and with (high risk) active malignancy at HSCT to ascertain the impact of disease status at HSCT on IR with fewer confounding effects from conditioning or T cell dosing. We analyzed IR at day +28 in patients receiving 2 step myeloablative haploidentical HSCT. All patients received 12 Gy of total body irradiation followed by 2 x 108 CD3+ cells/kg donor T cells (HSCT step 1). CY 60 mg/kg/d x 2 was given starting 2 or 3 days after the T cell infusion in the low and high risk groups respectively. Tacrolimus and MMF were begun on day -1. A CD 34 selected product was infused on day 0 (HSCT step 2) with median CD34 doses of 5.8 and 5.2 x 106/kg in the low and high-risk groups respectively. 19 patients with AML (9), ALL (7), MDS (1), and NHL (2) without disease, and 16 patients with AML (10), ALL (2), MDS (3), and T cell NHL (1) with active disease at HSCT were analyzed. A 17th patient in the high risk group died prior to engraftment and was not fully evaluable. Outcomes for the low and high risk groups respectively with 2-24 months follow-up (median of 9 in each group) were: no rejections; ANC >500: 11 versus 12 days; grades III-IV GVHD: 5.2% versus 18.7%; mortality from GVHD 0% versus 6.2%; infectious mortality: 0% versus 12.5%; non-infectious regimen-related mortality: 0% versus 11.7%; mortality from relapse; 5.2% versus 18.7%; Overall survival: 94.8% versus 52.9%. By day +28, all patients had achieved CR and >95% donor marrow chimerism. Compared to our experience with T cell depleted (TCD) HSCT, improved T and NK cell IR was observed, although the low risk group had higher median numbers of T cells. Conversely, higher numbers of CD56bright NK cells were present in the high risk group. Compared to TCD approaches at our institution and others, the 2 step approach allows for stronger early IR with low infectious mortality in patients without and with active malignancy at HSCT. IR was more robust in patients without active disease. IR in the higher risk group may be hindered by less hospitable marrow stroma and a greater baseline inflammation related to the active malignancy and exacerbated by the HSCT. The increased rate of significant GVHD and the prominence of NKbright cells, which are strong producers of cytokines, may reflect this higher state of inflammation. In addition, differences in the degree of T cell eradication by CY, based on T cell responses to malignancy or the longer period of T cell activation in the high risk regimen, may account for variations in IR between the groups. Recognition of the differences in early IR amongst specific patient populations may help optimize post HSCT care.