gebhart/patrepeval huggingface dataset:
Experimental Brain Injury Induces Regionally Distinct Apoptosis during the Acute and Delayed Post-Traumatic Period (1998)

The temporal pattern of apoptosis in the adult rat brain after lateral fluid-percussion (FP) brain injury was characterized using terminal deoxynucleotidyl-transferase-mediated biotin-dUTP nick end labeling (TUNEL) histochemistry and agarose gel electrophoresis. Male Sprague Dawley rats were subjected to brain injury and killed for histological analysis at intervals from 12 hr to 2 months after injury (n = 3/time point). Sham (uninjured) controls were subjected to anesthesia with (n = 3) or without (n = 3) surgery. Apoptotic TUNEL-positive cells were defined using stringent morphological criteria including nuclear shrinkage and fragmentation and condensation of chromatin and cytoplasm. Double-labeled immunocytochemistry was performed to identify TUNEL-positive neurons (anti-neurofilament monoclonal antibody RM044), astrocytes (anti-glial fibrillary acidic protein polyclonal antibody), and oligodendrocytes (anti-cyclic nucleotide phosphohydrolase polyclonal antibody). Compared with that seen with sham controls, in the injured cortex, significant apoptosis occurred at 24 hr (65 +/- 19 cells; p < 0.05) with a second, more pronounced response at 1 week after injury (91 +/- 24 cells; p < 0.05). The number of apoptotic cells in the white matter was increased as early as 12 hr after injury and peaked by 1 week (33 +/- 6 cells; p < 0.05). An increase in apoptotic cells was observed in the hippocampus at 48 hr (13 +/- 8), whereas in the thalamus, the apoptotic response was delayed, peaking at 2 weeks after injury (151 +/- 71 cells; p < 0.05). By 2 months, the number of apoptotic cells in most regions had returned to uninjured levels. At 24 hr after injury, TUNEL-labeled neurons and oligodendrocytes were localized primarily to injured cortex. By 1 week after injury, populations of TUNEL-labeled astrocytes and oligodendrocytes were present in the injured cortex, while double-labeled neurons were present predominantly in injured cortex and thalamus, with a few scattered in the hippocampus. DNA agarose gels confirmed morphological identification of apoptosis. These data suggest that the apoptotic response to trauma is regionally distinct and may be involved in both acute and delayed patterns of cell death.
Demineralized Bone: Implant Resorption With Long-term Follow-up (1990)

The osteoinductive properties of demineralized bone have stimulated its use in facial skeletal augmentation and reconstruction. Demineralized bone has been shown to induce phenotypic conversion of mesenchymal cells into osteoblasts, with bone formation within 29 days (osteoinduction). In this clinical study, 75 demineralized bone implants were followed up from 1 to 48 months (average follow-up, 14.3 months). There were 41 major dorsal implants, with an average degree of resorption of 50.7%. Eight dorsal implants were followed up for more than 24 months, with an 82.5% degree of resorption. Overall resorption for all implants was 49%. Major factors contributing to implant resorption included lack of surrounding mesenchymal cells and inadequate contact between host tissue and bone-inducing surface area. Other factors included infection, poor vascularity, and compression of the implant. Demineralized bone has an unacceptably high resorption rate and should only be used in highly selective cases where the implant can be positioned in a site rich in primitive mesenchymal or bone-forming cells.
The prevalence of verotoxins, Escherichia coli O157:H7, and Salmonella in the feces and rumen of cattle at processing. (1999)

Fecal samples collected from cattle at processing during a 1-year period were tested for verotoxins (VT1, VT2), Escherichia coli O157:H7, and Salmonella. Verotoxins were detected in 42.6% (95% CI, 39.8% to 45.4%), E. coli O157:H7 in 7.5% (95% CI, 6.1% to 9.1%), and Salmonella in 0.08% (95% CI, 0.004% to 0.5%) of the fecal samples. In yearling cattle, the median within-lot prevalence (percentage of positive samples within a lot) was 40% (range, 0% to 100%) for verotoxins and 0% for E. coli O157:H7 (range, 0% to 100%) and Salmonella (range, 0% to 17%). One or more fecal samples were positive for verotoxins in 80.4% (95% CI, 72.8% to 86.4%) of the lots of yearling cattle, whereas E. coli O157:H7 were detected in 33.6% (95% CI, 26.0% to 42.0%) of the lots. In cull cows, the median within-lot prevalence was 50% (range, 0% to 100%) for verotoxins and 0% (range, 0% to 100%) for E. coli O157:H7 and Salmonella (range, 0% to 0%). Verotoxins were detected in one or more fecal samples from 78.0% (95% CI, 70.4% to 84.2%) of the lots of cull cows, whereas E. coli O157:H7 were detected in only 6.0% (95% CI, 3.0% to 11.4%) of the lots of cull cows. The prevalence of verotoxins in fecal samples was lower in yearling cattle than in cull cows, whereas the prevalence of E. coli O157:H7 in fecal samples was higher in yearling cattle than in cull cows. The prevalence of E. coli O157:H7 in fecal samples was highest in the summer months. Rumen fill, body condition score, sex, type of cattle (dairy, beef), and distance travelled to the plant were not associated with the fecal prevalence of verotoxins or E. coli O157:H7. The prevalence of verotoxins in fecal samples of cull cows was associated with the source of the cattle. It was highest in cows from the auction market (52%) and farm/ranch (47%) and lowest in cows from the feedlot (31%). In rumen samples, the prevalence of verotoxins was 6.4% (95% CI, 4.2% to 9.4%), and it was 0.8% (95% CI, 0.2% to 2.3%) for E. coli O157:H7, and 0.3% (95% CI, 0.007% to 1.5%) for Salmonella.
Functional messenger RNAs are produced by SP6in vitrotranscription of cloned cDNAs (1984)

We describe a method for the synthesis of microgram quantities of eucaryotic messenger RNAs. Injection into the cytoplasm of frog oocytes and addition to wheat germ extracts show that these synthetic RNAs function efficiently as messenger RNAs. We confirm that a 5' cap on the mRNA is essential for translation in injected oocytes and show that most of the 3' flanking region, including the poly A tail, can be deleted without the abolition of protein synthesis. The method of mRNA synthesis involves in vitro transcription of cDNAs which have been cloned into SP6 vectors (described in the accompanying paper). This method enables one to produce large amounts of mRNA and consequently protein from any cDNA clone.
Peripheral B cell maturation. II. Heat-stable antigenhi splenic B cells are an immature developmental intermediate in the production of long-lived marrow-derived B cells. (1993)

HSAhi B cells comprise 5 to 10% of adult mouse splenic B cells and are phenotypically and functionally immature. To assess their origin and relationship to mature, heat-stable Ag (HSA)lo B cells, we determined HSA and surface IgD phenotype among splenic B cells throughout development, as well as during reconstitution of lethally irradiated adults given adult B-depleted bone marrow. In each case, HSAhi splenic B cells predominate during the earliest stages of B cell genesis. Furthermore, 5-bromo-2'-deoxyuridine labeling experiments indicate rapid turnover within both the marrow and peripheral HSAhi pools, and adoptive transfer studies show that peripheral HSAhi splenic B cells differentiate to HSAlo within 4 days. Finally, splenic HSAhi B cells reconstitute both primary and memory humoral responses. Together, these data indicate that splenic B cells in the HSAhi subset are an intermediate maturational stage in the adult periphery.
A solution to the simultaneous localization and map building (SLAM) problem (2001)

The simultaneous localization and map building (SLAM) problem asks if it is possible for an autonomous vehicle to start in an unknown location in an unknown environment and then to incrementally build a map of this environment while simultaneously using this map to compute absolute vehicle location. Starting from estimation-theoretic foundations of this problem, the paper proves that a solution to the SLAM problem is indeed possible. The underlying structure of the SLAM problem is first elucidated. A proof that the estimated map converges monotonically to a relative map with zero uncertainty is then developed. It is then shown that the absolute accuracy of the map and the vehicle location reach a lower bound defined only by the initial vehicle uncertainty. Together, these results show that it is possible for an autonomous vehicle to start in an unknown location in an unknown environment and, using relative observations only, incrementally build a perfect map of the world and to compute simultaneously a bounded estimate of vehicle location. The paper also describes a substantial implementation of the SLAM algorithm on a vehicle operating in an outdoor environment using millimeter-wave radar to provide relative map observations. This implementation is used to demonstrate how some key issues such as map management and data association can be handled in a practical environment. The results obtained are cross-compared with absolute locations of the map landmarks obtained by surveying. In conclusion, the paper discusses a number of key issues raised by the solution to the SLAM problem including suboptimal map-building algorithms and map management.
Multi-instance object segmentation with occlusion handling (2015)

We present a multi-instance object segmentation algorithm to tackle occlusions. As an object is split into two parts by an occluder, it is nearly impossible to group the two separate regions into an instance by purely bottomup schemes. To address this problem, we propose to incorporate top-down category specific reasoning and shape prediction through exemplars into an intuitive energy minimization framework. We perform extensive evaluations of our method on the challenging PASCAL VOC 2012 segmentation set. The proposed algorithm achieves favorable results on the joint detection and segmentation task against the state-of-the-art method both quantitatively and qualitatively.
Responsive Supramolecular Polymer Metallogel Constructed by Orthogonal Coordination-Driven Self-Assembly and Host/Guest Interactions (2014)

An emerging strategy for the fabrication of advanced supramolecular materials is the use of hierarchical self-assembly techniques wherein multiple orthogonal interactions between molecular precursors can produce new species with attractive properties. Herein, we unify the spontaneous formation of metal-ligand bonds with the host/guest chemistry of crown ethers to deliver a 3D supramolecular polymer network (SPN). Specifically, we have prepared a highly directional dipyridyl donor decorated with a benzo-21-crown-7 moiety that undergoes coordination-driven self-assembly with a complementary organoplatinum acceptor to furnish hexagonal metallacycles. These hexagons subsequently polymerize into a supramolecular network upon the addition of a bisammonium salt due to the formation of [2]pseudorotaxane linkages between the crown ether and ammonium moieties. At high concentrations, the resulting 3D SPN becomes a gel comprising many cross-linked metallohexagons. Notably, thermo- and cation-induced gel-sol transitions are found to be completely reversible, reflecting the dynamic and tunable nature of such supramolecular materials. As such, these results demonstrate the structural complexity that can be obtained when carefully controlling multiple interactions in a hierarchical fashion, in this case coordination and host/guest chemistry, and the interesting dynamic properties associated with the materials thus obtained.
MICROSTRIP BANDPASS FILTERS USING DUAL-MODE RESONATORS WITH INTERNAL COUPLED LINES (2011)

This paper presents a new dual-mode stub-loaded resonator, which consists of a microstrip resonator with internal coupled lines and an open-circuited stub. Based on the odd- and even-mode equivalent circuits, the resonant characteristics of the proposed microstrip resonator are investigated. It is found that the fundamental even-mode resonant frequency of the proposed resonator can be ∞exibly controlled while the fundamental odd-mode resonant frequency remains unafiected. Then, based on the proposed resonator, three compact dual-mode bandpass fllters, namely fller A, fllter B and fllter C, are designed, fabricated and measured to validate the design concept. Filters A and B demonstrate opposite asymmetric responses with two transmission poles in the passband and a transmission zero in the stopband. Filter C has three transmission poles in the passband and two transmission zeros respectively in the lower and upper stopbands to enhance selectivity. The experimental results show excellent agreement with the theoretical simulation results.
Altered fatty acid composition of lung surfactant phospholipids in interstitial lung disease (2002)

Deterioration of pulmonary surfactant function has been reported in interstitial lung disease; however, the molecular basis is presently unclear. We analyzed fatty acid (FA) profiles of several surfactant phospholipid classes isolated from large-surfactant aggregates of patients with idiopathic pulmonary fibrosis (IPF; n = 12), hypersensitivity pneumonitis (n = 5), and sarcoidosis (n = 12). Eight healthy individuals served as controls. The relative content of palmitic acid in phosphatidylcholine was significantly reduced in IPF (66.8 +/- 2.5%; means +/- SE; P < 0.01) but not in hypersensitivity pneumonitis (78.5 +/- 1.8%) and sarcoidosis (78.2 +/- 3.1%; control 80.1 +/- 0.7%). In addition, the phosphatidylglycerol FA profile was significantly altered in the IPF patients, with a lower relative content of its major FA, oleic acid, at the expense of saturated FA. In the phosphatidylcholine class, a significant correlation between the impairment of biophysical surfactant function and decreased percentages of palmitic acid was noted. We conclude that significant alterations in the FA profile of pulmonary surfactant phospholipids occur predominantly in IPF and may contribute to the disturbances of alveolar surface activity in this disease.
Tumor Microenvironment Complexity: Emerging Roles in Cancer Therapy (2012)

The tumor microenvironment (TME) consists of cells, soluble factors, signaling molecules, extracellular matrix, and mechanical cues that can promote neoplastic transformation, support tumor growth and invasion, protect the tumor from host immunity, foster therapeutic resistance, and provide niches for dormant metastases to thrive. An American Association for Cancer Research (AACR) special conference held on November 3-6, 2011, addressed five emerging concepts in our understanding of the TME: its dynamic evolution, how it is educated by tumor cells, pathways of communication between stromal and tumor cells, immunomodulatory roles of the lymphatic system, and contribution of the intestinal microbiota. These discussions raised critical questions on how to include the analysis of the TME in personalized cancer diagnosis and treatment.
An EMFi-film sensor based ballistocardiographic chair: performance and cycle extraction method (2006)

New sensor technologies open possibilities for measuring traditional biosignals in new innovative ways. This, together with the development of signal processing systems and their computing power, can sometimes give new life to old measurement techniques. Ballistocardiogram is one such technique, originally promising but quickly replaced by the now very popular electrocardiogram. A ballistocardiograph chair, designed to look like a normal office chair, was built and fitted with pressure sensitive EMFi-films. The films are connected via a charge amplifier to a medical bioamplifier. The system was accepted for medical use in Tampere University Hospital and patient measurements have been performed. The system is presented and it's performance evaluated. A wireless version of the system is needed to hide the cabling from the user. This makes the chair indistinguishable from a normal office chair. Overview of first wireless prototype is given. To analyze recorded BCG, individual BCG cycles must be extracted from the signal containing respiration and movement artifacts. A method for this and results of it's application are presented. The developed system can be used for BCG measurements and it is able to automatically extract individual BCG cycles, but it has some limitations which are presented in the paper.
Using multimodal information for the segmentation of fluorescent micrographs with application to Virology and microbiology (2011)

In order to improve reproducibility and objectivity of fluorescence microscopy based experiments and to enable the evaluation of large datasets, flexible segmentation methods are required which are able to adapt to different stainings and cell types. This adaption is usually achieved by the manual adjustment of the segmentation methods parameters, which is time consuming and challenging for biologists with no knowledge on image processing. To avoid this, parameters of the presented methods automatically adapt to user generated ground truth to determine the best method and the optimal parameter setup. These settings can then be used for segmentation of the remaining images. As robust segmentation methods form the core of such a system, the currently used watershed transform based segmentation routine is replaced by a fast marching level set based segmentation routine which incorporates knowledge on the cell nuclei. Our evaluations reveal that incorporation of multimodal information improves segmentation quality for the presented fluorescent datasets.
Second-Line Treatment of Ovarian Cancer (2000)

Patients with epithelial ovarian cancer are often diagnosed with advanced-stage disease. Although clinical complete remissions are obtained in the majority of patients through a combination of cytoreductive surgery and chemotherapy, relapse is common. A number of agents with diverse biologic mechanisms have been identified with activity in the setting of recurrent disease. Strategies for management of patients with recurrent disease, including classification, treatment goals, and therapeutic options will be reviewed.
Conceptual Database Design: An Entity-Relationship Approach (1991)

I. CONCEPTUAL DATABASE DESIGN. 1. An Introduction to Database Design. 2. Data Modeling Concepts. 3. Methodologies for Conceptual Design. 4. View Design. 5. View Integration. 6. Improving the Quality of a Database Schema. 7. Schema Documentation and Maintenance. II. FUNCTIONAL ANALYSIS FOR DATABASE DESIGN. 1. Functional Analysis Using the Dataflow Model. 2. Joint Data and Functional Analysis. 3. Case Study. III. LOGICAL DESIGN AND DESIGN TOOLS. 1. High-Level Logical Design Using the Entity-Relationship Model. 2. Logical Design for the Relational Model. 3. Logical Design for the Network Model. 4. Logical Design for the Hierarchical Model. 5. Database Design Tools. Index. 0805302441T04062001
Structure and function of Norrin in assembly and activation of a Frizzled 4–Lrp5/6 complex (2013)

Norrin is a cysteine-rich growth factor that is required for angiogenesis in the eye, ear, brain, and female reproductive organs. It functions as an atypical Wnt ligand by specifically binding to the Frizzled 4 (Fz4) receptor. Here we report the crystal structure of Norrin, which reveals a unique dimeric structure with each monomer adopting a conserved cystine knot fold. Functional studies demonstrate that the novel Norrin dimer interface is required for Fz4 activation. Furthermore, we demonstrate that Norrin contains separate binding sites for Fz4 and for the Wnt ligand coreceptor Lrp5 (low-density lipoprotein-related protein 5) or Lrp6. Instead of inducing Fz4 dimerization, Norrin induces the formation of a ternary complex with Fz4 and Lrp5/6 by binding to their respective extracellular domains. These results provide crucial insights into the assembly and activation of the Norrin-Fz4-Lrp5/6 signaling complex.
A Novel Mutant Gene Involved in T-Lymphocyte–Specific Homing Into Peripheral Lymphoid Organs on Mouse Chromosome 4 (1998)

Previously, we have shown a mutant mouse DDD/1 with T-cell-specific homing defect that is regulated by an autosomal recessive gene, plt (paucity of lymph node T cells), and seems to be caused by lymph node (LN) stromal cells. In the present study, immunohistochemical analysis showed unusual distribution of T cells in LN, Peyer's patches (PP), and spleen from plt/plt, probably due to the failure of T cells to migrate from blood into the T-cell zone in LN or PP, or into the spleen white pulp across high endothelial venule or marginal zone, respectively, based on the experiments in which labelled T cells were injected intravenously and detected in the tissues. Analysis of surface L-selectin and CD44 suggested that T cells with memory phenotype, probably from afferent lymphatics, recruit into plt/plt LN. Linkage mapping by simple-sequence length polymorphism of genomic DNA from 190 backcross progenies produced by intercrossing with MSM/Ms, linked plt most closely with D4Mit237, and localized at 24.7 cM from cetromere on chromosome 4. We discuss the possibility that a wild-type gene on plt locus encodes a chemokine inducing T-cell-specific homing into peripheral lymphoid tissues.
INCB16562, a JAK1/2 Selective Inhibitor, Is Efficacious against Multiple Myeloma Cells and Reverses the Protective Effects of Cytokine and Stromal Cell Support (2010)

Cytokines in the bone marrow of multiple myeloma patients activate Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathways in tumor cells and promote tumor growth, survival, and drug resistance. INCB16562 was developed as a novel, selective, and orally bioavailable small-molecule inhibitor of JAK1 and JAK2 markedly selective over JAK3. The specific cellular activity of the inhibitor was demonstrated by its potent and dose-dependent inhibition of cytokine-dependent JAK/STAT signaling and cell proliferation in the absence of effects on Bcr-Abl-expressing cells. Treatment of myeloma cells with INCB16562 potently inhibited interleukin-6 (IL-6)-induced phosphorylation of STAT3. Moreover, the proliferation and survival of myeloma cells dependent on IL-6 for growth, as well as the IL-6-induced growth of primary bone marrow-derived plasma cells from a multiple myeloma patient, were inhibited by INCB16562. Induction of caspase activation and apoptosis was observed and attributed, at least in part, to the suppression of Mcl-1 expression. Importantly, INCB16562 abrogated the protective effects of recombinant cytokines or bone marrow stromal cells and sensitized myeloma cells to cell death by exposure to dexamethasone, melphalan, or bortezomib. Oral administration of INCB16562 antagonized the growth of myeloma xenografts in mice and enhanced the antitumor activity of relevant agents in combination studies. Taken together, these data suggest that INCB16562 is a potent JAK1/2 inhibitor and that mitigation of JAK/STAT signaling by targeting JAK1 and JAK2 will be beneficial in the treatment of myeloma patients, particularly in combination with other agents.
Animal Studies Journal 2017 6 (1): Cover Page, Table of Contents, Editorial and Notes on Contributors (2017)

Animal Studies Journal 2017 6 (1): Cover Page, Table of Contents, Editorial and Notes on Contributors.