gebhart/patrepeval huggingface dataset:
An NKT-mediated autologous vaccine generates CD4 T-cell–dependent potent antilymphoma immunity (2007)

Relapses occurring in most patients with lymphoma after antibody or chemotherapy highlight a need for effective vaccination approaches. Autologous tumors are ideal sources of patient-specific tumor antigens for vaccines; however, their poor immunogenicity has been a major obstacle in practice. Natural killer T (NKT) cells have recently emerged as crucial regulators of autoimmunity and tumor immunosurveillance. Here, we show that an autologous lymphoma vaccine that activates NKT cells generated tumor-specific protective immunity in experimental mice. Single vaccination with alpha-galactosylceramide (alphaGC)-loaded A20 lymphoma cells elicited effective antitumor immunity against tumor challenge. This vaccination strategy also induced significant tumor regression in A20-bearing mice. Importantly, the survivors from primary tumor inoculation were all resistant to tumor rechallenge, indicative of established adaptive memory immunity. Depletion as well as adoptive transfer studies revealed an exclusive role of conventional CD4(+) but not CD8(+) T cells in mediating antitumor immunity. In addition, we found normal hematopoietic compartments in the vaccinated mice. Therefore, NKT ligand-loaded lymphoma elicits long-lasting and effective antitumor immunity, which can be further developed as patient- and tumor-specific immunotherapy against human lymphomas.
Experimental mycobacteriosis in striped bass Morone saxatilis (2003)

Striped bass Morone saxatilis were infected intraperitoneally with approximately 10(5) Mycobacterium marinum, M. shottsii sp. nov., or M. gordonae. Infected fish were maintained in a flow-through freshwater system at 18 to 21 degrees C, and were examined histologically and bacteriologically at 2, 4, 6, 8, 17, 26, 36 and 45 wk post-infection (p.i.). M. marinum caused acute peritonitis, followed by extensive granuloma development in the mesenteries, spleen and anterior kidney. Granulomas in these tissues underwent a temporal progression of distinct morphological stages, culminating in well-circumscribed lesions surrounded by normal or healing tissue. Mycobacteria were cultured in high numbers from splenic tissue at all times p.i. Standard Ziehl-Neelsen staining, however, did not demonstrate acid-fast rods in most early inflammatory foci and granulomas. Large numbers of acid-fast rods were present in granulomas beginning at 8 wk p.i. Between 26 and 45 wk p.i., reactivation of disease was observed in some fish, with disintegration of granulomas, renewed inflammation, and elevated splenic bacterial densities approaching 10(9) colony-forming units g(-1). Infection with M. shottsii or M. gordonae did not produce severe pathology. Mild peritonitis was followed by granuloma formation in the mesenteries, but, with 1 exception, granulomas were not observed in the spleen or anterior kidney. M. shottsii and M. gordonae both established persistent infections in the spleen, but were present at densities at least 2 orders of magnitude less than M. marinum at all time points observed. Granulomas in the mesenteries of M. shottsii- and M. gordonae-infected fish resolved over time, and no reactivation of disease was observed.
High-speed functional OCT with self-reconstructive Bessel illumination at 1300 nm (2011)

We present a Bessel beam illumination FDOCT setup with FDML buffered swept source at 1300nm. An extended focus is achieved due to the Bessel beam that preserves its lateral extend over a large depth range. Decoupling the illumination from the Gaussian detection improves the sensitivity as compared to double passing the ring filter and enables dark field imaging. Dark field imaging is useful to avoid strong reflexes from the sample's surface that adversely affect the sensitivity due to the limited dynamic range of high-speed 8bit acquisition cards. Furthermore, Bessel beams exhibit a self-reconstruction property that allows imaging even behind obstacles such as hairs on skin. Densely sampled volumes of skin in-vivo with high lateral resolution are acquired at up to 440kHz A-Scan rate. In addition the possibility of contrasting capillaries with high sensitivity is shown, using inter-B-scan speckle variance analysis. High-speed imaging is of crucial importance for imaging small details since sample motion artifacts are reduced and high sampling can be maintained while increasing the B-Scan rate.
A Bifunctional Bacterial Protein Links GDI Displacement to Rab1 Activation (2007)

Rab guanosine triphosphatases (GTPases) regulate vesicle trafficking in eukaryotic cells by reversibly associating with lipid membranes. Inactive Rab GTPases are maintained in the cytosol by binding to GDP-dissociation inhibitor (GDI). It is believed that specialized proteins are required to displace GDI from Rab GTPases before Rab activation by guanosine diphosphate-guanosine 5'-triphosphate (GDP-GTP) exchange factors (GEFs). Here, we found that SidM from Legionella pneumophila could act as both GEF and GDI-displacement factor (GDF) for Rab1. Rab1 released from GDI was inserted into liposomal membranes and was used as a substrate for SidM-mediated nucleotide exchange. During host cell infection, recruitment of Rab1 to Legionella-containing vacuoles depended on the GDF activity of SidM. Thus, GDF and GEF activity can be promoted by a single protein, and GDF activity can coordinate Rab1 recruitment from the GDI-bound pool.
Therapeutic Peptides and Proteins (2005)

Upon publication of the first edition of Therapeutic Peptides and Proteins ten years ago there were only 19 biotechology medicines on the market. Currently there are more than 100, with at least 400 more in various stages of development. That alone would be grounds for a new edition. Add to that the fact that it is still difficult to find up
A microdeletion of less than 250 kb, including the proximal part of the FMR-I gene and the fragile-X site, in a male with the clinical phenotype of fragile-X syndrome. (1992)

A gene designated "FMR-1" has been isolated at the fragile-X locus. One exon of this gene is carried on a 5.1-kb EcoRI fragment that exhibits length variation in fragile-X patients because of amplification of or insertion into a CGG-repeat sequence. This repeat probably represents the fragile site. The EcoRI fragment also includes an HTF island that is hypermethylated in fragile-X patients showing absence of FMR-1 mRNA. In this paper, we present further evidence that the FMR-1 gene is involved in the clinical manifestation of the fragile-X syndrome and also in the expression of the cellular phenotype. A deletion including the HTF island and exons of the FMR-1 gene was detected in a fragile X-negative mentally retarded male who presented the clinical phenotype of the fragile-X syndrome. The deletion involves less than 250 kb of genomic DNA, including DXS548 and at least five exons of the FMR-1 gene. These data support the hypothesis that loss of function of the FMR-1 gene leads to the clinical phenotype of the fragile-X syndrome. In the fragile-X syndrome, there are pathogenetic mechanisms other than amplification of the CGG repeat that do have the same phenotypic consequences.
Fast atom bombardment mass spectrometry of two isomeric tripeptides (1981)

Abstract Fast atom bombardment of solids is presented as the basis of a new ion source for mass spectrometry. This novel technique is particularly useful for obtaining mass spectra from involatile and thermally labile materials. The ion source produces both positive and negative ions with equal facility, and examples of both are presented for two underivatized tripeptides. The normal second field free region metastables are observed in a double focusing mass spectrometer and comprehensive metastable pathways have been traced using Barber‐Elliott (V‐scan) techniques.
PROMALS web server for accurate multiple protein sequence alignments (2007)

Multiple sequence alignments are essential in homology inference, structure modeling, functional prediction and phylogenetic analysis. We developed a web server that constructs multiple protein sequence alignments using PROMALS, a progressive method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment accuracy than other advanced methods, such as MUMMALS, ProbCons, MAFFT and SPEM. The PROMALS web server takes FASTA format protein sequences as input. The output includes a colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation. The PROMALS web server is available at: http://prodata.swmed.edu/promals/
The prognostic significance of sialyl-tn Antigen in women treated with breast carcinoma treated with adjuvant chemotherapy (1997)

The results of this study suggest that STn may be a valuable marker for identifying women at high risk of developing recurrent breast carcinoma who may be candidates for trials investigating new therapies in combination with standard adjuvant therapy.
SLAM and its role in T cell activation and Th cell responses (1997)

Following the initial events of T cell activation, triggered by binding of specific peptide-MHC complex to the TCR for antigen and engagement of costimulatory molecules, a number of activation molecules are expressed on the cell surface. Many of these molecules regulate T cell function, T-T cell interactions and the interaction of T cells with other cells. One such molecule is SLAM, a multifunctional 70 kDa glycoprotein member of the Ig superfamily with multiple isoforms. SLAM is rapidly induced on naive T cells and B cells following activation. Engagement of SLAM by a specific antibody (mAb A12) results in IL-2-independent T cell expansion and induction/up-regulation of IFN-gamma by activated T cells, including Th2 cells. SLAM was found to be a high-affinity self-ligand mediating molecular and cellular homophilic interactions. In this review we discuss SLAM as a receptor involved in T cell expansion and in directing immune responses to a Th0-Th1 pathway.
Olig2 Overexpression Induces the In Vitro Differentiation of Neural Stem Cells into Mature Oligodendrocytes (2005)

Differentiation induction of neural stem cells (NSCs) into oligodendrocytes during embryogenesis is the result of a complex interaction between local induction factors and intracellular transcription factors. At the early stage of differentiation, in particular, the helix-loop-helix transcription factors Olig1 and Olig2 have been shown to be essential for oligodendrocyte lineage determination. In view of the possible application of NSCs as a source for remyelinating cell transplants in demyelinating diseases (e.g., multiple sclerosis), in vitro procedures need to be developed to drive the oligodendrocyte differentiation process. Mere culture in medium supplemented with major embryonic oligodendrogenic induction factors, such as Sonic hedgehog, results in oligodendrocyte differentiation of only about 10% of NSCs. We previously showed that induction of Olig1 expression by gene transfection could indeed initiate the first stage of oligodendrocyte differentiation in NSCs, but appeared to be unable to generate fully mature, functional oligodendrocytes. In this study, we transfected NSCs isolated from the embryonic mouse brain with the Olig2 gene and found that the introduced overexpression of Olig2 could induce the development of fully mature oligodendrocytes expressing the transcription factor Nkx2.2 and all major myelin-specific proteins. Moreover, Olig2-transfected NSCs, in contrast to nontransfected NSCs, developed into actively remyelinating oligodendrocytes after transplantation into the corpus callo-sum of long-term cuprizonefed mice, an animal model for demyelination. Our results show that transfection of genes encoding for oligodendrogenic transcription factors can be an efficient way to induce the differentiation of NSCs into functional oligodendrocytes.
Linking molecular therapeutics to molecular diagnostics: Inhibition of the FRAP/RAFT/TOR component of the PI3K pathway preferentially blocks PTEN mutant cells in vitro and in vivo (2001)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Multiscale Roughness and Stability of Superhydrophobic Biomimetic Interfaces (2007)

The stability of a composite interface of roughness-induced superhydrophobic surfaces is studied. To have high contact angle and low contact angle hysteresis, superhydrophobic surfaces should be able to form a composite interface with air pockets in the valleys between asperities (pillars). However, the composite interface may be unstable and can be irreversibly transformed into a homogeneous interface. We formulate a stability criterion and analyze the stability of the composite interface for several typical roughness profiles. To resist destabilizing mechanisms, multiscale (hierarchical) roughness is required. Such multiscale roughness is found in natural and artificial superhydrophobic surfaces.
Phase-sensitive amplification in a fiber (2004)

Phase-sensitive amplification (PSA) has the potential to improve significantly the performance of optical communication systems. PSA is known to occur in chi(2) devices, and in a fiber interferometer, which is an example of a chi(3) device. In this report some four-wave mixing processes are described, which produce PSA directly in fibers.
Hedgehog signal pathway is activated in ovarian carcinomas, correlating with cell proliferation: It's inhibition leads to growth suppression and apoptosis (2006)

The hedgehog (Hh) signal pathway has recently been shown to be activated in human malignancies. However, little is known about its role in the development or patient prognosis of epithelial ovarian carcinoma. In the present study, we examined in vivo and in vitro the expression and functional role of Hh signal molecules in epithelial ovarian tumors and normal ovarian surface epithelial (OSE) cells. The expression of Shh, Dhh, Ptch, Smo and Gli1 proteins was not observed in normal OSE, but was increased stepwise in benign, borderline and malignant neoplasms. In addition, immunoreactivity for Shh, Dhh, Ptch, Smo and Gli1 was highly correlated with cell proliferation assessed by Ki-67. Blocking the Hh signal using either the Hh pathway inhibitor cyclopamine or Gli1 siRNA led to remarkably decreased cell proliferation in ovarian carcinoma cells. Treatment with cyclopamine induced not only G, arrest but also apoptosis along with the downregulation of cyclin A and cyclin D1, and the upregulation of p21 and p27. Among the Hh signal molecules, Dhh expression was correlated with poor prognosis of ovarian carcinoma patients. These findings suggest that the Hh signal pathway plays an important role in ovarian tumorigenesis as well as in the activation of cell proliferation in ovarian carcinomas. Thus, the Hh signal pathway is a possible molecular target of new treatment strategies for ovarian carcinoma.
False-positive screening results in the Finnish prostate cancer screening trial (2010)

An FP result is a common adverse effect of PC screening and affects at least every eighth man screened repeatedly, even when using a relatively high cutoff level. False-positive men constitute a special group that receives unnecessary interventions but may harbour missed cancers. New strategies are needed for risk stratification in PC screening to minimise the proportion of FP men.
GLP‐1 derivative liraglutide in rats with β‐cell deficiencies: influence of metabolic state on β‐cell mass dynamics (2003)

(1) Liraglutide is a long-acting GLP-1 derivative, designed for once daily administration in type II diabetic patients. To investigate the effects of liraglutide on glycemic control and beta-cell mass in rat models of beta-cell deficiencies, studies were performed in male Zucker diabetic fatty (ZDF) rats and in 60% pancreatectomized rats. (2) When liraglutide was dosed s.c. at 150 microg kg-1 b.i.d. for 6 weeks in ZDF rats 6-8 weeks of age at study start, diabetes development was markedly attenuated. Blood glucose was approximately 12 mm lower compared to vehicle (P<0.0002), and plasma insulin was 2-3-fold higher during a normal 24-h feeding period (P<0.001). Judged by pair feeding, approximately 53% of the antihyperglycemic effect observed on 24-h glucose profiles was mediated by a reduction in food intake, which persisted throughout the study and averaged 16% (P<0.02). (3) Histological analyses revealed that beta-cell mass and proliferation were significantly lower in prediabetic animals still normoglycemic after 2 weeks treatment compared to vehicle-treated animals that had begun to develop diabetes. When the treatment period was 6 weeks, the liraglutide-treated animals were no longer completely normoglycemic and the beta-cell mass was significantly increased compared to overtly diabetic vehicle-treated animals, while beta-cell proliferation was unaffected. (4) In the experiments with 60% pancreatectomized rats, 8 days treatment with liraglutide resulted in a significantly lower glucose excursion in response to oral glucose compared to vehicle treatment. Again, part of the antihyperglycemic effect was due to reduced food intake. No effect of liraglutide on beta-cell mass was observed in these virtually normoglycemic animals. (5) In conclusion, treatment with liraglutide has marked antihyperglycemic effects in rodent models of beta-cell deficiencies, and the in vivo effect of liraglutide on beta-cell mass may in part depend on the metabolic state of the animals.
Action bank: A high-level representation of activity in video (2012)

Activity recognition in video is dominated by low- and mid-level features, and while demonstrably capable, by nature, these features carry little semantic meaning. Inspired by the recent object bank approach to image representation, we present Action Bank, a new high-level representation of video. Action bank is comprised of many individual action detectors sampled broadly in semantic space as well as viewpoint space. Our representation is constructed to be semantically rich and even when paired with simple linear SVM classifiers is capable of highly discriminative performance. We have tested action bank on four major activity recognition benchmarks. In all cases, our performance is better than the state of the art, namely 98.2% on KTH (better by 3.3%), 95.0% on UCF Sports (better by 3.7%), 57.9% on UCF50 (baseline is 47.9%), and 26.9% on HMDB51 (baseline is 23.2%). Furthermore, when we analyze the classifiers, we find strong transfer of semantics from the constituent action detectors to the bank classifier.
The Potential Predictive Value of Cyclooxygenase-2 Expression and Increased Risk of Gastrointestinal Hemorrhage in Advanced Non–Small Cell Lung Cancer Patients Treated with Erlotinib and Celecoxib (2008)

The combination of erlotinib and celecoxib does not seem superior to erlotinib alone in unselected patients. However, longer PFS with high-tumor COX-2 expression suggests that trials of EGFR and COX-2 inhibitors may be warranted in this patient subset. GIB observed in our trial supports excluding patients with a history of peptic ulcer disease or those requiring therapeutic anticoagulation from future EGFR and COX-2 inhibitor studies.
Diabetic Neuropathies (2005)

The diabetic neuropathies are heterogeneous, affecting different parts of the nervous system that present with diverse clinical manifestations. They may be focal or diffuse. Most common among the neuropathies are chronic sensorimotor distal symmetric polyneuropathy (DPN) and the autonomic neuropathies. DPN is a diagnosis of exclusion. The early recognition and appropriate management of neuropathy in the patient with diabetes is important for a number of reasons. 1 ) Nondiabetic neuropathies may be present in patients with diabetes. 2 ) A number of treatment options exist for symptomatic diabetic neuropathy. 3 ) Up to 50% of DPN may be asymptomatic, and patients are at risk of insensate injury to their feet. As >80% of amputations follow a foot ulcer or injury, early recognition of at-risk individuals, provision of education, and appropriate foot care may result in a reduced incidence of ulceration and consequently amputation. 4 ) Autonomic neuropathy may involve every system in the body. 5 ) Autonomic neuropathy causes substantial morbidity and increased mortality, particularly if cardiovascular autonomic neuropathy (CAN) is present. Treatment should be directed at underlying pathogenesis. Effective symptomatic treatments are available for the manifestations of DPN and autonomic neuropathy.

This statement is based on two recent technical reviews (1,2), to which the reader is referred for detailed discussion and relevant references to the literature.

An internationally agreed simple definition of DPN for clinical practice is “the presence of symptoms and/or signs of peripheral nerve dysfunction in people with diabetes after the exclusion of other causes” (3). However, the diagnosis cannot be made without a careful clinical examination of the lower limbs, as absence of symptoms should never be assumed to indicate an absence of signs. This definition conveys the important message that not all patients with peripheral nerve dysfunction have a neuropathy caused by diabetes. Confirmation can be established with …
Topology inference from BGP routing dynamics (2002)

This paper describes a method of inferring logical relationships between network prefixes within an Autonomous System (AS) using only passive monitoring of BGP messages. By clustering these prefixes based upon similarities between their update times, we create a hierarchy linking the prefixes within the larger AS. We can frequently identify groups of prefixes routed to the same ISP Point of Presence (POP), despite the lack of identifying information in the BGP messages. Similarly, we observe disparate prefixes under common organizational control, or with long shared network paths. In addition to discovering interesting network characteristics, our passive method facilitates topology discovery by potentially reducing the number of active probes required in traditional traceroute-based Internet mapping mechanisms.
Amorphous Photonic Crystals with Only Short‐Range Order (2013)

Distinct from conventional photonic crystals with both short- and long-range order, amorphous photonic crystals that possess only short-range order show interesting optical responses owing to their unique structural features. Amorphous photonic crystals exhibit unique light scattering and transport, which lead to a variety of interesting phenomena such as isotropic photonic bandgaps or pseudogaps, noniridescent structural colors, and light localization. Recent experimental and theoretical advances in the study of amorphous photonic crystals are summarized, focusing on their unique optical properties, artificial fabrication, bionspiration, and potential applications.