gebhart/patrepeval huggingface dataset:
The generation of nisin variants with enhanced activity against specific Gram‐positive pathogens (2008)

Nisin is the prototype of the lantibiotic group of antimicrobial peptides. It exhibits broad spectrum inhibition of gram-positive bacteria including important food pathogens and clinically relevant antibiotic-resistant bacteria. Significantly, the gene-encoded nature of nisin means that it can be subjected to gene-based bioengineering to generate novel derivatives. Here, we take advantage of this to generate the largest bank of randomly mutated nisin derivatives reported to date, with the ultimate aim of identifying variants with enhanced bioactivity. This approach led to the identification of a nisin-producing strain with enhanced bioactivity against the mastitic pathogen Streptococcus agalactiae resulting from an amino acid change in the hinge region of the peptide (K22T). Prompted by this discovery, site-directed and site-saturation mutagenesis of the hinge region residues was employed, resulting in the identification of additional derivatives, most notably N20P, M21V and K22S, with enhanced bioactivity and specific activity against gram-positive pathogens including Listeria monocytogenes and/or Staphylococcus aureus. The identification of these derivatives represents a major step forward in the bioengineering of nisin, and lantibiotics in general, and confirms that peptide engineering can deliver derivatives with enhanced antimicrobial activity against specific problematic spoilage and pathogenic microbes or against gram-positive bacteria in general.
Laparoscopic hysterectomy using laparosonic coagulating shears: experience of 15 cases. (2000)

In conventional laparoscopic hysterectomy, adequate hemostasis is provided by bipolar coagulation, staple, and suture. The Laparosonic Coagulating Shears (LCS) have been proven to give both hemostasis and cutting. The objective of this study was to evaluate the efficacy of the LCS for laparoscopic hysterectomy. Fifteen patients indicated for hysterectomy were enrolled for laparoscopic hysterectomy using LCS. Each procedure was performed under general endotracheal anesthesia. The LCS were operated at power level 1 though 5. All pedicles, blood vessels, and tissues were coagulated and cut by LCS. The cardinal ligaments were cut and ligated transvaginally. The uterus was removed through the vagina. The operative finding, uterine volume and weight, operative time, CO2 volume, blood loss and hospital stay were recorded. Among the 15 cases, the indications were myoma uteri (7 cases), adenomyosis (6 cases) and adenomyosis with endometriomas (2 cases). The mean volume of the uterus was 226.8 cm3 (range 77-399 cm3) and mean weight was 188.8 g (range 85-320 g). Mean operative time was 171.6 min (range 114-210 min) and CO2 loss was 313.8 liters (range 120-650 liters). Blood loss was 366.7 ml (range 100-1,500 ml). LCS can be used for coagulation and cutting simultaneously. Minimal charring and smoke was observed during operation. In general, the hospital stay was 3 days (range 2-4 days), except for one case of recto-sigmoid injury and 2 cases of ureteric injury when the hospital stay was 7, 10, and 12 days, respectively. The injuries occurred in cases with anatomic distortion, profuse bleeding, and dense adhesion. LCS can be used as an alternative instrument for coagulation and dissection. According to our experience, it produces less charring and smoke compared to electrocoagulation. However, a high rate of complications were still encountered.
Application of Transcription-Mediated Amplification to Quantification of Gene Sequences (1998)

To be useful in clinical settings, hybridization-based assays must have high specificity and adequate sensitivity to detect clinically relevant concentrations of nucleic acid, and must be easy to use. Processing of patient specimens for these assays should involve a minimal number of steps so that the entire assay procedure will fit easily into the clinical laboratory.
STRONG ASSOCIATION BETWEEN THE RESPONDER STATUS OF THE FCγ II RECEPTOR and RECURRENT SPONTANEOUS ABORTION (1995)

Several models exist for the aetiology and therapy of recurrent spontaneous abortion (RSA). They are based in part on the assumption that an increased materno-fetal histocompatibility results in an insufficient maternal immunological recognition of the fetus, and thus renders the maternal immune system unable to sustain the pregnancy. The involvement of the FcgammaII receptor (FcgammaIIR) in RSA was suggested, since FcgammaIIR-blocking antibodies, present in normal pregnancies, could not be found in patients suffering from RSA. The FcgammaIIR is known to be functionally and structurally dimorphic, which results in a responder, respectively non-responder pattern. We used an in vitro proliferation assay to distinguish between FcgammaIIR responder and non-responder phenotypes. In 29 RSA couples we found 97% (28/29) of RSA patients and 100% (29/29) of their partners to be responders, whereas 50 fertile couples and a further 100 unrelated controls revealed distributions of responder vs. non-responder of 73% vs. 27% and 70% vs. 30%, respectively. These differences (RSA vs. controls) are highly significant (P less than or equal to 0.0001). Our results suggest further that the FcgammaIIR dimorphism might be involved in the pathogenesis of RSA.
Essential Role for the SMN Complex in the Specificity of snRNP Assembly (2002)

The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). Using cell extracts and purified components, we demonstrated that the SMN complex is necessary and sufficient to mediate the ATP-dependent assembly of the core of seven Sm proteins on uridine-rich, small nuclear ribonucleic acids (U snRNAs). In vitro experiments revealed strict requirements for ordered binding of the Sm proteins and the U snRNAs to the SMN complex. Importantly, the SMN complex is necessary to ensure that Sm cores assemble only on correct RNA targets and prevent their otherwise promiscuous association with other RNAs. Thus, the SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, nonspecific binding of Sm proteins to RNAs.
CTLA-4 is constitutively expressed on tumor cells and can trigger apoptosis upon ligand interaction (2005)

CTLA-4 (CD152) is a cell surface receptor that behaves as a negative regulator of the proliferation and the effector function of T cells. We have previously shown that CTLA-4 is also expressed on neoplastic lymphoid and myeloid cells, and it can be targeted to induce apoptosis. In our study, we have extended our analysis and have discovered that surface expression of CTLA-4 is detectable by flow cytometry on 30 of 34 (88%) cell lines derived from a variety of human malignant solid tumors including carcinoma, melanoma, neuroblastoma, rhabdomyosarcoma and osteosarcoma (but not in primary osteoblast-like cultures). However, by reverse transcriptase-PCR, CTLA-4 expression was detected in all cell lines. We have also found, by immunohistochemistry, cytoplasmic and surface expression of CTLA-4 in the tumor cells of all 6 osteosarcoma specimens examined and in the tumour cells of all 5 cases (but only weakly or no positivity at all in neighbouring nontumor cells) of ductal breast carcinomas. Treatment of cells from CTLA-4-expressing tumor lines with recombinant forms of the CTLA-4-ligands CD80 and CD86 induced apoptosis associated with sequential activation of caspase-8 and caspase-3. The level of apoptosis was reduced by soluble CTLA-4 and by anti-CTLA-4 scFvs antibodies. The novel finding that CTLA-4 molecule is expressed and functional on human tumor cells opens up the possibility of antitumor therapeutic intervention based on targeting this molecule.
Histologic Comparison of Light Emitting Diode Phototherapy-Treated Hydroxyapatite-Grafted Extraction Sockets: A Same-Mouth Case Study (2007)

The accelerated bone healing in the phototherapy-treated HA socket graft may provide faster implant placement compared to non-phototherapy-treated socket grafts.
Quantitative Analysis of Intestinal Bacterial Populations From Term Infants Fed Formula Supplemented With Fructo‐oligosaccharides (2012)

The milk-based formula used in this study supported bifidobacterial and lactobacilli populations comparable with the human milk group; however, this formula did not suppress E coli or C difficile as effectively as human milk.
Suppression of angiogenesis, tumorigenicity, and metastasis by human prostate cancer cells engineered to produce interferon-beta. (1999)

We determined whether the IFN-beta gene can be used to suppress angiogenesis, tumor growth, and metastasis of human prostate cancer cells growing in the prostate of nude mice. Highly metastatic PC-3M human prostate cancer cells were engineered to constitutively produce murine IFN-beta subsequent to infection with a retroviral vector containing murine IFN-beta cDNA. Parental (PC-3M-P), control vector-transduced (PC-3M-Neo), and IFN-beta-transduced (PC-3M-IFN-beta) cells were injected into the prostate (orthotopic) or subcutis (ectopic) of nude mice. PC-3M-P and PC-3M-Neo cells produced rapidly growing tumors and regional lymph node metastases, whereas PC-3M-IFN-beta cells did not. PC-3M-IFN-beta cells also suppressed the tumorigenicity of bystander nontransduced prostate cancer cells. PC-3M-IFN-beta cells produced small tumors (3-5 mm in diameter) in nude mice treated with anti-asialo GM1 antibodies and in severe combined immunodeficient/Beige mice. Immunohistochemical staining revealed that PC-3M-IFN-beta tumors were homogeneously infiltrated by macrophages, whereas control tumors contained fewer macrophages at their periphery. Most tumor cells in the control tumors were stained positive by an antibody to proliferative cell nuclear antigen; very few were positively stained by terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling. In sharp contrast, PC-3M-IFN-beta tumors contained fewer proliferative cell nuclear antigen-positive cells and many terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling-positive cells. Staining with antibody against CD31 showed that control tumors contained more blood vessels than PC-3M-IFN-beta tumors. PC-3M-IFN-beta cells were more sensitive to lysis mediated by natural killer cells in vitro or to cytostasis mediated by macrophages than control transduced cells. Conditioned medium from PC-3M-IFN-beta cells augmented splenic cell-mediated cytolysis to control tumor cells, which could be neutralized by antibody against IFN-beta. Collectively, the data suggest that the suppression of tumorigenicity and metastasis of PC-3M-IFN-beta cells is due to inhibition of angiogenesis and activation of host effector cells.
Chromosome 18 DNA markers and manic-depressive illness: evidence for a susceptibility gene. (1994)

In the course of a systematic genomic survey, 22 manic-depressive (bipolar) families were examined for linkage to 11 chromosome 18 pericentromeric marker loci, under dominant and recessive models. Overall logarithm of odds score analysis for the pedigree series was not significant under either model, but several families yielded logarithm of odds scores consistent with linkage under dominant or recessive models. Affected sibling pair analysis of these data yielded evidence for linkage (P < 0.001) at D18S21. Affected pedigree member analysis also suggests linkage, with multilocus results for five loci giving P < 0.0001 and P = 0.0007 for weighting functions f(p) = 1 and 1/square root p, respectively, where p is the allele frequency. These results imply a susceptibility gene in the pericentromeric region of chromosome 18, with a complex mode of inheritance. Two plausible candidate genes, a corticotropin receptor and the alpha subunit of a GTP binding protein, have been localized to this region.
Epidemiology of Age-related Maculopathy (1995)

Journal Article Epidemiology of Age-related Maculopathy Get access Johannes R. Vingerling, Johannes R. Vingerling 1Department of Ophthalmology, Erasmus University Medical schoolRotterdam, The Netherlands2Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Caroline C. W. Klaver, Caroline C. W. Klaver 1Department of Ophthalmology, Erasmus University Medical schoolRotterdam, The Netherlands2Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Albert Hofman, Albert Hofman 2Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Paulus T. V. M. de Jong Paulus T. V. M. de Jong 1Department of Ophthalmology, Erasmus University Medical schoolRotterdam, The Netherlands2Department of Epidemiology and Biostatistics, Erasmus University Medical SchoolRotterdam, The Netherlands3The Netherlands Ophthalmic Research InstituteAmsterdam, The Netherlands Prof. T. V. M. de Jong, The Netherlands Ophthalmic Research Institute, P.O. Box 12141, 1100 AC Amsterdam, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Epidemiologic Reviews, Volume 17, Issue 2, 1995, Pages 347–360, https://doi.org/10.1093/oxfordjournals.epirev.a036198 Published: 01 July 1995 Article history Received: 05 December 1994 Published: 01 July 1995 Accepted: 03 October 1995
Comparison of Newer Laparoscopic Port Closure Techniques in the Porcine Model (1995)

Obtaining a precise fascial closure of larger laparoscopic port sites presents an ongoing challenge for even the most experienced laparoscopic surgeons. To this end, we evaluated five new methods for closing laparoscopic port sites and compared these with the standard technique of a hand-sutured repair using a 0 absorbable suture in the pig. The new devices studied were the Carter-Thomason Needle-Point Suture Passer (CTNSP), the eXit Disposable Puncture Closure (EDPC) device, the Maciol suture needle (MSN) set, the Endoclose suture carrier, and a nonpropreitary technique using a long 14-gauge Angiocatheter and a looped Prolene suture. Unlike the typical clinical situation, the fascia of the pig lies extremely close to the skin; hence, the sutured closure could be routinely performed most quickly of all. Among the newer techniques, the CTNSP provided the quickest closure. The Endoclose, MSN, and 14-gauge Angiocatheter techniques required the use of an auxiliary grasper, which appeared to slow the closure. Only the EDPC provided an airtight closure in 100% of cases. Of the new techniques, the 14-gauge Angiocatheter technique was the least expensive ($3). The efficacy of these techniques in the clinical realm needs to be assessed by a randomized trial.
ShieldTester: Cell‐to‐Cell Visibility Test for Surface Occluders (2003)

Abstract We present a novel Cell‐To‐Cell Visibility (C2CV) algorithm, which given two polyhedra , A and B and a connectedand oriented manifold triangle mesh, S offers a simple, fast and conservative test for detecting when A and B areoccluded from each other by S . Previously disclosed C2CV algorithms either relied on costly occlusion fusion orwere restricted to convex or “apparently convex” occluders, which makes them inappropriate for scenes wherepotential occluders are arbitrary triangulated surfaces, such as the body of a car or a portion of a terrain. Thesimplicity of our C2CV algorithm, named ShieldTester, stems from a new Occlusion Theorem, introduced herewhich permits to establish occlusion by computing the intersection of S with a single ray from a vertex of A toa vertex of B . ShieldTester may be used to establish that pairs of cells in a subdivision of space are hidden fromeach other by a relatively large surface occluder, so that when the viewer is in one cell, the objects in the othercell need not be displayed. Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Computational Geometryand Object Modeling: Occlussion Culling, Visibility Test, Triangle Meshes
Neurological Deterioration in Acute Ischemic Stroke (1999)

In the setting of a multicenter trial, EPS and LPS are mainly related to computed tomographic signs of cerebral edema. Treatment with recombinant tissue plasminogen activator, hemorrhagic transformation, and moderate changes in systolic blood pressure did not influence the early clinical course.
Introduction (1998)

The chapter identifies satiation as a negative feedback process of control during a meal and depends on peripheral and central mechanisms for the detection, transmission, processing, and integration of the chemical and mechanical stimuli of the ingested food. Sherrington (1947) emphasized that satiation is an example of the kind of active inhibitory process necessary for central neural integration and is stimulated by ingested food which inhibits eating. Numerous techniques used to analyse the negative feedback produced by ingested food reveals that satiation is elicited primarily by mechanical and chemical food stimuli acting on specific receptors in mucosa lining the mouth, esophagus, stomach, and upper small intestine, and involves spatial and mechanistic synergistic interactions.
Spatiotemporal Profiles of Field Potentials in Mouse Superior Colliculus Analyzed by Multichannel Recording (2008)

The onset and vector of orienting behaviors, such as saccades, are controlled by commands that descend from a population of neurons in deep layers of the superior colliculus (dSC). In this study, to characterize the role of the collicular local circuitry that generates the spatiotemporal pattern of command activity in the dSC neuronal population, responses evoked by single-pulse electrical stimulation in superficial layers of the superior colliculus (sSC) were analyzed by a 64-channel field potential recording system (planar electrode, 8 x 8 pattern; 150 microm interelectrode spacing) in slices obtained from 16- to 22-d-old mice. A negative field potential with short latency and short duration spatially restricted to the recording sites in sSC was evoked adjacent to the stimulation site. After bath application of 10 mum bicuculline, the same stimulus induced a large negative field response with long duration that spread from sSC to dSC. The dSC potential initially showed a positive response, presumably because of reversal of the negative potential that originated in sSC, and then a long negative response that spread horizontally as far as 1 mm. These responses disappeared after application of an NMDA receptor antagonist, 2-amino-5-phosphonovelarate, indicating that NMDA receptors have an important role in the generation of these responses. Simultaneous whole-cell patch-clamp recordings showed that the long-lasting negative field potentials corresponded to the depolarization accompanying burst spike activity of SC neurons. The present study revealed an extensive excitatory network in the dSC that may contribute to the generation of activity by a large population of neurons that discharge before a saccade.
Human genetic diseases : a practical approach (1986)

Abbreviations Fetal DNA analysis A short guide to linkage analysis The use of synthetic olignucleotides as specific hybridization probes in the diagnosis of genetic disorders Alternative methods of gene diagnosis Fine mapping of genes: the characterization of the transcriptional unit In situ hybridization Human chromosome analysis by flow cytometry Restriction analysis of chromosomal DNA in a size range up to two million base pairs by pulsed field gradient electrophoresis Appendix Index
Healing Times and Prediction of Wound Healing in Neuropathic Diabetic Foot Ulcers: a Prospective Study (2005)

Time line of wound healing and prediction of healing times in diabetic foot ulcers is an important issue. Usually, the percentage of wounds healed within a defined period is used for characterization of wound healing. R=sqrtA/pi (R, radius; A, planimetric wound area; pi, constant 3.14), and the wound radius reduction was 0.39 mm/week which was previously established. The initial average wound area was 96.9+/-13.1 mm2 (mean+/-SEM), and 3.61+/-1.6 mm 2 after ten weeks with an average healing time of 75.9 (95 %-CI 71-81) days. Using the equation mentioned above and the calculated weekly wound radius reduction, the predicted healing time in the test group was 86.9 (95 %-CI 73-101) days. The predicted and the observed healing times were significantly correlated with each other (r=0.55, p=0.0002). Providing standard care, the time needed for wound healing can reliably be predicted in neuropathic diabetic foot ulcers. This may be a useful tool in daily clinical practice to predict wound healing and recognize ulcers who do not respond adequately to the treatment.
B-Allyldiisocaranylborane: a new, remarkable enantioselective allylborating agent for prochiral aldehydes. Synthesis of homoallylic alcohols approaching 100% enantiomeric purities (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTB-Allyldiisocaranylborane: a new, remarkable enantioselective allylborating agent for prochiral aldehydes. Synthesis of homoallylic alcohols approaching 100% enantiomeric puritiesHerbert C. Brown and Prabhakar K. JadhavCite this: J. Org. Chem. 1984, 49, 21, 4089–4091Publication Date (Print):October 1, 1984Publication History Published online1 May 2002Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/jo00195a052https://doi.org/10.1021/jo00195a052research-articleACS PublicationsRequest reuse permissionsArticle Views523Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Low-Latency Video Semantic Segmentation (2018)

Recent years have seen remarkable progress in semantic segmentation. Yet, it remains a challenging task to apply segmentation techniques to video-based applications. Specifically, the high throughput of video streams, the sheer cost of running fully convolutional networks, together with the low-latency requirements in many real-world applications, e.g. autonomous driving, present a significant challenge to the design of the video segmentation framework. To tackle this combined challenge, we develop a framework for video semantic segmentation, which incorporates two novel components: (1) a feature propagation module that adaptively fuses features over time via spatially variant convolution, thus reducing the cost of per-frame computation; and (2) an adaptive scheduler that dynamically allocate computation based on accuracy prediction. Both components work together to ensure low latency while maintaining high segmentation quality. On both Cityscapes and CamVid, the proposed framework obtained competitive performance compared to the state of the art, while substantially reducing the latency, from 360 ms to 119 ms.