gebhart/patrepeval huggingface dataset:
Concave Urinary Crystallines: Direct Evidence of Calcium Oxalate Crystals Dissolution by CitrateIn Vivo (2013)

The changes in urinary crystal properties in patients with calcium oxalate (CaOx) calculi after oral administration of potassium citrate (K3cit) were investigated via atomic force microscopy (AFM), scanning electron microscopy (SEM), X-ray powder diffractometry (XRD), and zeta potential analyzer. The AFM and SEM results showed that the surface of urinary crystals became concave, the edges and corners of crystals became blunt, the average size of urinary crystallines decreased significantly, and aggregation of urinary crystals was reduced. These changes were attributed to the significant increase in concentration of excreted citrate to 492 ± 118 mg/L after K3cit intake from 289 ± 83 mg/L before K3cit intake. After the amount of urinary citrate was increased, it complexed with Ca(2+) ions on urinary crystals, which dissolved these crystals. Thus, the appearance of concave urinary crystals was a direct evidence of CaOx dissolution by citrate in vivo. The XRD results showed that the quantities and species of urinary crystals decreased after K3cit intake. The mechanism of inhibition of formation of CaOx stones by K3cit was possibly due to the complexation of Ca(2+) with citrate, increase in urine pH, concentration of urinary inhibitor glycosaminoglycans (GAGs), and the absolute value of zeta potential after K3cit intake.
Enhancing breast tumor detection with near-field imaging (2002)

This article outlines the main features of active, passive, and hybrid systems under investigation for breast cancer detection. Our main focus is on active microwave systems, in particular microwave tomography and confocal microwave imaging.
Daratumumab yields rapid and deep hematologic responses in patients with heavily pretreated AL amyloidosis (2017)

The majority of patients with immunoglobulin light chain amyloidosis (AL) fail to achieve a complete response (CR) to standard light chain suppressive chemotherapy, and almost all patients eventually experience hematologic relapse and progression of organ involvement. Additional well-tolerated treatment options are needed. We present our retrospective experience of 25 consecutive previously treated AL patients who received daratumumab, a CD38-directed monoclonal antibody approved for the treatment of multiple myeloma. Daratumumab was administered at 16 mg/kg weekly for 8 weeks, then every 2 weeks for 8 doses, and then every 4 weeks. Patients had received a median of 3 prior lines of therapy, with a previous hematologic CR in only 5 patients. The overall hematologic response rate to daratumumab was 76%, including CR in 36% and very good partial response in 24%. Median time to response was 1 month. Therapy was well tolerated, even among the 72% of patients with cardiac AL involvement. Grade 1-2 infusion reactions occurred in 15 patients, but no grade 3 or 4 reactions were observed. Daratumumab is a highly effective agent that produced rapid and deep hematologic responses without unexpected toxicity in our cohort of heavily pretreated AL patients.
Gross and Microscopic Lesions in Porcine Fetuses Infected with Porcine Reproductive and Respiratory Syndrome Virus (1996)

Diagnosis of porcine reproductive and respiratory syndrome virus (PRRSV)-induced reproductive failure in swine is difficult because of the rapid inactivation of virus in fetuses that have died prior to abortion or farrowing. In this report, we describe gross and microscopic lesions of diagnostic value found in fetuses transplacentally infected with PRRSV during late gestation. Seven sows free of PRRSV-specific antibody and 1 sow (#8) that had been previously infected with PRRSV were oronasally exposed to a PRRSV inoculum at or about 90 days of gestation (DG). One control sow (#9) was oronasally exposed to a sham inoculum at 90 DG. Sows were euthanized 21 days postexposure, and fetuses were tested for virus. Transplacental infection was detected in litters 1-7, and gross lesions of the umbilical cord were observed in some fetuses in 6 of the 7 litters. No transplacental infection or fetal lesions were found in litters 8 and 9. The gross lesions in the umbilical cords ranged from segmental hemorrhagic areas 1-2 cm in length to a full length involvement of the cord, which was grossly distended with frank hemorrhage. All live fetuses that had gross lesions in the umbilical cord were viremic, and histopathologic examination revealed a necrotizing umbilical arteritis with periarterial hemorrhage. This was the most consistent microscopic lesion in fetuses infected with PRRSV. Sows 1-7 had endometritis and myometritis of various degrees, suggesting PRRSV also may induce these lesions. Careful gross and microscopic examination of the umbilical cord may aid in the diagnosis of PRRSV-induced reproductive failure.
Myofibroblasts and the progression of diabetic nephropathy (1997)

We have demonstrated in this study the neoexpression of cytoskeletal proteins within diabetic kidneys. This has allowed the identification of new predicting histological markers for the progression of diabetic nephropathy.
Genomic Organization of Human and Mouse Genes for Vascular Endothelial Growth Factor C (1997)

We report here the cloning and characterization of human and mouse genes for vascular endothelial growth factor C (VEGF-C), a newly isolated member of the vascular endothelial growth factor/platelet-derived growth factor (VEGF/PDGF) family. Both VEGF-C genes comprise over 40 kilobase pairs of genomic DNA and consist of seven exons, all containing coding sequences. The VEGF homology domain of VEGF-C is encoded by exons 3 and 4. Exons 5 and 7 encode cysteine-rich motifs of the type C6C10CRC, and exon 6 encodes additional C10CXCXC motifs typical of a silk protein. A putative alternatively spliced rare RNA form lacking exon 4 was identified in human fibrosarcoma cells, and a major transcription start site was located in the human VEGF-C gene 523 base pairs upstream of the translation initiation codon. The upstream promoter sequences contain conserved putative binding sites for Sp-1, AP-2, and NF-kappaB transcription factors but no TATA box, and they show promoter activity when transfected into cells. The VEGF-C gene structure is thus assembled from exons encoding propeptides and distinct cysteine-rich domains in addition to the VEGF homology domain, and it shows both similarities and distinct differences in comparison with other members of the VEGF/PDGF gene family.
Zoonotic Vaccinia Virus: Clinical and Immunological Characteristics in a Naturally Infected Patient (2008)

Vaccinia virus was used as vaccine to eradicate smallpox. We report a zoonotic case of vaccinia virus infection in a 30-year-old patient who became infected after handling sick dairy cattle. The patient had inflamed lesions and systemic symptoms. Laboratory findings were indicative of down-modulated immune responses to the virus.
Synergism between a Novel Chimeric Lysin and Oxacillin Protects against Infection by Methicillin-Resistant Staphylococcus aureus (2010)

Staphylococcus aureus is the causative agent of several serious infectious diseases. The emergence of antibiotic-resistant S. aureus strains has resulted in significant treatment difficulties, intensifying the need for new antimicrobial agents. Toward this end, we have developed a novel chimeric bacteriophage (phage) lysin that is active against staphylococci, including methicillin-resistant S. aureus (MRSA). The chimeric lysin (called ClyS) was obtained by fusing the N-terminal catalytic domain of the S. aureus Twort phage lysin with the C-terminal cell wall-targeting domain from another S. aureus phage lysin (phiNM3), which displayed Staphylococcus-specific binding. ClyS was expressed in Escherichia coli, and the purified protein lysed MRSA, vancomycin-intermediate strains of S. aureus (VISA), and methicillin-sensitive (MSSA) strains of S. aureus in vitro. In a mouse nasal decolonization model, a 2-log reduction in the viability of MRSA cells was seen 1 h following a single treatment with ClyS. One intraperitoneal dose of ClyS also protected against death by MRSA in a mouse septicemia model. ClyS showed a typical pattern of synergistic interactions with both vancomycin and oxacillin in vitro. More importantly, ClyS and oxacillin at doses that were not protective individually protected synergistically against MRSA septic death in a mouse model. These results strongly support the development of ClyS as an attractive addition to the current treatment options of multidrug-resistant S. aureus infections and would allow for the reinstatement of antibiotics shelved because of mounting resistance.
Cerebral White Matter Is Highly Vulnerable to Ischemia (1996)

These results suggest that the cerebral white matter is highly vulnerable to the effects of focal ischemia. Pathological changes in oligodendrocytes and myelinated axons appear early and seem to be concomitant with, but independent of neuronal perikaryal injury. Modifications of this experimental model of focal ischemia could provide the means to test the hypothesis that selected types of human leukoencephalopathies have an ischemic origin.
Beyond the HPA Axis: Progesterone-Derived Neuroactive Steroids in Human Stress and Emotion (2011)

Stress and social isolation are well-known risk factors for psychopathology. However, more research is needed as to the physiological mechanisms by which social support buffers the impacts of stress. Research in animal models suggests important roles for progesterone (P) and its product, the neuroactive steroid allopregnanolone (ALLO), in stress and psychopathology. These hormones are produced in brain and periphery during stress in rodents, and down-regulate anxiety behavior and hypothalamic-pituitary-adrenal axis activity. Human clinical populations, including depressed patients, have alterations in ALLO levels, but it is unclear whether these basal hormone level differences have clinical import. To begin to address this question, this review examines the role of P and ALLO in stress physiology, and the impact of these hormones on mood, in healthy humans. Evidence largely supports that P and ALLO increase during stress in humans. However, P/ALLO administration appears to cause only mild effects on mood and subjective anxiety, while exerting effects consistent with gamma-aminobutyric acid receptor modulation. Additionally, P is linked to motivation for affiliation/social contact; P (and ALLO) release may be especially responsive to social rejection. These observations lead to the novel hypothesis that stress-related P/ALLO production functions not only to down-regulate stress and anxiety, but also to promote social contact as a long-term coping strategy. Malfunctioning of the P/ALLO system could therefore underlie depression partly by decreasing propensity to affiliate with others.
Carbon nanotube-based ethanol sensors (2009)

Sensors containing metal-carbon nanotube (CNT) hybrid materials as the active sensing layer were demonstrated for ethanol vapor detection at room temperature. The metal-CNT hybrid materials were synthesized by infiltrating single wall carbon nanotubes (SWNTs) with the transition metals Ti, Mn, Fe, Co, Ni, Pd or Pt. Each sensor was prepared by drop-casting dilute dispersions of a metal-CNT hybrid onto quartz substrate electrodes and the impedimetric responses to varying ethanol concentration were recorded. Upon exposure to ethanol vapor, the ac impedance (Z') of the sensors was found to decrease to different extents. The sensor containing pristine CNT material was virtually non-responsive at low ethanol concentrations (<50 ppm). In contrast, all metal-CNT hybrid sensors showed extremely high sensitivity to trace ethanol levels with 100-fold or more gains in sensitivity relative to the starting SWNT sensor. All hybrid sensors, with the exception of Ni filled CNT, exhibited significantly larger sensor responses to ethanol vapor up to 250 ppm compared to the starting SWNT sensor.
Noninvasive Brain Stimulation Improves Language Learning (2008)

Anodal transcranial direct current stimulation (tDCS) is a reliable technique to improve motor learning. We here wanted to test its potential to enhance associative verbal learning, a skill crucial for both acquiring new languages in healthy individuals and for language reacquisition after stroke-induced aphasia. We applied tDCS (20 min, 1 mA) over the posterior part of the left peri-sylvian area of 19 young right-handed individuals while subjects acquired a miniature lexicon of 30 novel object names. Every subject participated in one session of anodal tDCS, one session of cathodal tDCS, and one sham session in a randomized and double-blinded design with three parallel versions of the miniature lexicon. Outcome measures were learning speed and learning success at the end of each session, and the transfer to the subjects' native language after the respective stimulation. With anodal stimulation, subjects showed faster and better associative learning as compared to sham stimulation. Mood ratings, reaction times, and response styles were comparable between stimulation conditions. Our results demonstrate that anodal tDCS is a promising technique to enhance language learning in healthy adults and may also have the potential to improve language reacquisition after stroke.
Disseminated Vaccinia in a Military Recruit with Human Immunodeficiency Virus (HIV) Disease (1987)

LIVE-VIRUS vaccines have been well recognized as a cause of severe complications when inadvertently administered to recipients with impaired immunologic function.1 The acquired immunodeficiency syndrome (AIDS) has been recognized as a severe immunodeficiency state caused by infection with a retrovirus, human immunodeficiency virus (HIV).2 HIV infection and disease include a wide spectrum of clinical presentations, such as asymptomatic infections, chronic generalized lymphadenopathy, and frank T-cell deficiency (AIDS-related complex and AIDS).3 Although the natural history of HIV infection has only been partly defined, it is clear that patients with AIDS represent only a minority of the total number of T-cell–deficient patients . . .
Chemical chaperones mediate increased secretion of mutant α1-antitrypsin (α1-AT) Z: A potential pharmacological strategy for prevention of liver injury and emphysema in α1-AT deficiency (2000)

In alpha1-AT deficiency, a misfolded but functionally active mutant alpha1-ATZ (alpha1-ATZ) molecule is retained in the endoplasmic reticulum of liver cells rather than secreted into the blood and body fluids. Emphysema is thought to be caused by the lack of circulating alpha1-AT to inhibit neutrophil elastase in the lung. Liver injury is thought to be caused by the hepatotoxic effects of the retained alpha1-ATZ. In this study, we show that several "chemical chaperones," which have been shown to reverse the cellular mislocalization or misfolding of other mutant plasma membrane, nuclear, and cytoplasmic proteins, mediate increased secretion of alpha1-ATZ. In particular, 4-phenylbutyric acid (PBA) mediated a marked increase in secretion of functionally active alpha1-ATZ in a model cell culture system. Moreover, oral administration of PBA was well tolerated by PiZ mice (transgenic for the human alpha1-ATZ gene) and consistently mediated an increase in blood levels of human alpha1-AT reaching 20-50% of the levels present in PiM mice and normal humans. Because clinical studies have suggested that only partial correction is needed for prevention of both liver and lung injury in alpha1-AT deficiency and PBA has been used safely in humans, it constitutes an excellent candidate for chemoprophylaxis of target organ injury in alpha1-AT deficiency.
Effect of storage upon material properties of lyophilized porcine extracellular matrix derived from the urinary bladder (2005)

Xenogeneic extracellular matrices (ECMs) have been developed as off-the-shelf biologic scaffolds that have been effectively used in preclinical and clinical applications for tissue reconstruction. Such materials must be suitable for terminal sterilization and capable of storage for extended periods of time without significant changes in material properties and bioactivity. Material properties of interest for ECM scaffolds include hydrostatic permeability index (PI), uniaxial maximum load and elongation, maximum tangential stiffness (MTS), suture retention strength (SRS), and ball-burst strength (BBS). The present study evaluated these material properties for lyophilized forms of an ECM scaffold derived from the porcine urinary bladder, termed urinary bladder matrix (UBM), that was terminally sterilized by e-beam irradiation at 22 kGy and stored at room temperature (RT; 20-24 degrees C) or refrigerated temperature (REFT; 4-8 degrees C) for up to 12 months. UBM devices showed no change in SRS, BBS, and hydrostatic PI after the evaluation period. Lyophilized devices stored at RT showed an increase in maximum load and MTS while devices stored at REFT showed an increase in maximum elongation after 1 year of storage (p < 0.05). These results indicate that structural changes in the UBM device may slowly occur as a function of prolonged storage and storage temperature.
A 3-D Microfluidic Combinatorial Cell Culture Array (2009)

We present the development of a three-dimensional (3-D), on-glass combinatorial cell culture array chip featured with integrated three-input, eight-output combinatorial mixers and cell culture chambers. The device is designed to simultaneously screen for the effects of multiple compounds and concentrations on cultured cells. Experimentally, we first developed a precise way to characterize the combined compound concentration profile at each chamber with a fluorescence method. We then successfully demonstrated the functionality of the cell assay by culturing neuron cells on this device and screening the ability of three chemicals to attenuate cell death caused by cytotoxic hydrogen peroxide. Based on the same technology, the number of inputs and outputs of the combinatorial mixer can be scaled-up to construct lab-on-chip devices for performing high-throughput cell-based assay and highly parallel and combinatorial chemical or biochemical reactions with reduced labors, reagents, and time.
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation (2010)

The indigenous human microbiota is essential to the health of the host. Although the microbiota can be affected by many features of modern life, we know little about its responses to disturbance, especially repeated disturbances, and how these changes compare with baseline temporal variation. We examined the distal gut microbiota of three individuals over 10 mo that spanned two courses of the antibiotic ciprofloxacin, analyzing more than 1.7 million bacterial 16S rRNA hypervariable region sequences from 52 to 56 samples per subject. Interindividual variation was the major source of variability between samples. Day-to-day temporal variability was evident but constrained around an average community composition that was stable over several months in the absence of deliberate perturbation. The effect of ciprofloxacin on the gut microbiota was profound and rapid, with a loss of diversity and a shift in community composition occurring within 3-4 d of drug initiation. By 1 wk after the end of each course, communities began to return to their initial state, but the return was often incomplete. Although broadly similar, community changes after ciprofloxacin varied among subjects and between the two courses within subjects. In all subjects, the composition of the gut microbiota stabilized by the end of the experiment but was altered from its initial state. As with other ecosystems, the human distal gut microbiome at baseline is a dynamic regimen with a stable average state. Antibiotic perturbation may cause a shift to an alternative stable state, the full consequences of which remain unknown.
Program slicing with dynamic points-to sets (2005)

Program slicing is a potentially useful analysis for aiding program understanding. However, in reality even slices of small programs are often too large to be useful. Imprecise pointer analyses have been suggested as one cause of this problem. In this paper, we use dynamic points-to data, which represents optimistic pointer information, to obtain a bound on the best case slice size improvement that can be achieved with improved pointer precision. Our experiments show that slice size can be reduced significantly for programs that make frequent use of calls through function pointers because for them the dynamic pointer data results in a considerably smaller call graph, which leads to fewer data dependences. Programs without or with only few calls through function pointers, however, show considerably less improvement. We discovered that C programs appear to have a significant fraction of direct and nonspurious pointer data dependences so that reducing spurious dependences via pointers is only of limited benefit. Consequently, to make slicing useful in general for such programs, improvements beyond better pointer analyses are necessary. On the other hand, since we show that collecting dynamic function pointer information can be performed with little overhead (average slowdown of 10 percent for our benchmarks), dynamic pointer information may be a practical approach to making slicing of programs with frequent function pointer use more successful in practice.
Notch Signaling in Cancer (2002)

Notch signaling plays a key role in the normal development of many tissues and cell types, through diverse effects on differentiation, survival, and/or proliferation that are highly dependent on signal strength and cellular context. Because perturbations in the regulation of differentiation, survival, and/or proliferation underlie malignant transformation, pathophysiologic Notch signals potentially contribute to cancer development in several different ways. Notch signaling was first linked to tumorigenesis through identification of a recurrent t(7;9)(q34;q34.3) chromosomal translocation involving the human Notch1 gene that is found in a small subset of human pre-T-cell acute lymphoblastic leukemias (T-ALL).(1) Since this discovery, aberrant Notch signaling has been suggested to be involved in a wide variety of human neoplasms. In this review, we will focus on recent studies linking aberrant Notch signaling with cancer. First, we discuss various mechanisms through which Notch signaling may influence cellular transformation. Then, we critically review literature pertaining to the role of Notch signaling in several cancers, and discuss possible therapeutic targets in the Notch pathway.
Therapeutic potential of 90Y- and 131I-labeled anti-CD20 monoclonal antibody in treating non-Hodgkin's lymphoma with pulmonary involvement: a Monte Carlo-based dosimetric analysis. (2007)

Monte Carlo-based dosimetry was performed to compare the therapeutic potential of (90)Y and (131)I targeting of lung metastases in NHL patients. (131)I provided a therapeutic advantage over (90)Y, especially in tumors with radii less than 2.0 cm and at lower tumor burdens. For both (90)Y- and (131)I-labeled antibodies, treatment is more efficacious when applied to metastatic NHL cases with lower tumor burdens. (131)I has advantages over (90)Y in treating smaller lung metastases.