gebhart/patrepeval huggingface dataset:
Broadly cross-reactive HIV-1-neutralizing human monoclonal Fab selected for binding to gp120–CD4–CCR5 complexes (2002)

HIV-1 entry into cells involves formation of a complex between gp120 of the viral envelope glycoprotein (Env), a receptor (CD4), and a coreceptor, typically CCR5. Here we provide evidence that purified gp120(JR-FL)-CD4-CCR5 complexes exhibit an epitope recognized by a Fab (X5) obtained by selection of a phage display library from a seropositive donor with a relatively high broadly neutralizing serum antibody titer against an immobilized form of the trimolecular complex. X5 bound with high (nM) affinity to a variety of Envs, including primary isolates from different clades and Envs with deleted variable loops (V1, -2, -3). Its binding was significantly increased by CD4 and slightly enhanced by CCR5. X5 inhibited infection of peripheral blood mononuclear cells by a selection of representative HIV-1 primary isolates from clades A, B, C, D, E, F, and G with an efficiency comparable to that of the broadly neutralizing antibody IgG1 b12. Furthermore, X5 inhibited cell fusion mediated by Envs from R5, X4, and R5X4 viruses. Of the five broadly cross-reactive HIV-1-neutralizing human monoclonal antibodies known to date, X5 is the only one that exhibits increased binding to gp120 complexed with receptors. These findings suggest that X5 could possibly be used as entry inhibitor alone or in combination with other antiretroviral drugs for the treatment of HIV-1-infected individuals, provide evidence for the existence of conserved receptor-inducible gp120 epitopes that can serve as targets for potent broadly cross-reactive neutralizing antibodies in HIV-1-infected patients, and have important conceptual and practical implications for the development of vaccines and inhibitors.
Targeted treatment of advanced and metastatic breast cancer with lapatinib (2008)

Improved molecular understanding of breast cancer in recent years has led to the discovery of important drug targets such as HER-2 and EGFR. Lapatinib is a potent dual inhibitor of HER-2 and EGFR. Preclinical and phase I studies have shown activity with lapatinib in a number of cancers, including breast cancer, and the drug is well tolerated. The main known drug interactions are with paclitaxel and irinotecan. The most significant side-effects of lapatinib are diarrhea and adverse skin events. Rates of cardiotoxicity compare favorably with trastuzumab, a monoclonal antibody against HER-2. This paper focuses on lapatinib in advanced and metastatic breast cancer, which remains an important therapeutic challenge. Phase II and III studies show activity as monotherapy, and in combination with chemotherapy or hormonal agents. Results from these studies suggest that the main benefit from lapatinib is in the HER-2 positive breast cancer population. Combinations of lapatinib and trastuzumab are also being studied and show encouraging results, particularly in trastuzumab-refractory metastatic breast cancer. Lapatinib may have a specific role in treating HER-2 positive CNS metastases. The role of lapatinib as neoadjuvant therapy and in early breast cancer is also being evaluated.
MerTK inhibition in tumor leukocytes decreases tumor growth and metastasis (2013)

MerTK, a receptor tyrosine kinase (RTK) of the TYRO3/AXL/MerTK family, is expressed in myeloid lineage cells in which it acts to suppress proinflammatory cytokines following ingestion of apoptotic material. Using syngeneic mouse models of breast cancer, melanoma, and colon cancer, we found that tumors grew slowly and were poorly metastatic in MerTK-/- mice. Transplantation of MerTK-/- bone marrow, but not wild-type bone marrow, into lethally irradiated MMTV-PyVmT mice (a model of metastatic breast cancer) decreased tumor growth and altered cytokine production by tumor CD11b+ cells. Although MerTK expression was not required for tumor infiltration by leukocytes, MerTK-/- leukocytes exhibited lower tumor cell-induced expression of wound healing cytokines, e.g., IL-10 and growth arrest-specific 6 (GAS6), and enhanced expression of acute inflammatory cytokines, e.g., IL-12 and IL-6. Intratumoral CD8+ T lymphocyte numbers were higher and lymphocyte proliferation was increased in tumor-bearing MerTK-/- mice compared with tumor-bearing wild-type mice. Antibody-mediated CD8+ T lymphocyte depletion restored tumor growth in MerTK-/- mice. These data demonstrate that MerTK signaling in tumor-associated CD11b+ leukocytes promotes tumor growth by dampening acute inflammatory cytokines while inducing wound healing cytokines. These results suggest that inhibition of MerTK in the tumor microenvironment may have clinical benefit, stimulating antitumor immune responses or enhancing immunotherapeutic strategies.
SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features (2014)

Whole-genome and exome sequencing studies reveal many genetic variants between individuals, some of which are linked to disease. Many of these variants lead to single amino acid variants (SAVs), and accurate prediction of their phenotypic impact is important. Incorporating sequence conservation and network-level features, we have developed a method, SuSPect (Disease-Susceptibility-based SAV Phenotype Prediction), for predicting how likely SAVs are to be associated with disease. SuSPect performs significantly better than other available batch methods on the VariBench benchmarking dataset, with a balanced accuracy of 82%. SuSPect is available at www.sbg.bio.ic.ac.uk/suspect. The Web site has been implemented in Perl and SQLite and is compatible with modern browsers. An SQLite database of possible missense variants in the human proteome is available to download at www.sbg.bio.ic.ac.uk/suspect/download.html.
Advances in PCR technology (2004)

Since the discovery of the polymerase chain reaction (PCR) 20 years ago, an avalanche of scientific publications have reported major developments and changes in specialized equipment, reagents, sample preparation, computer programs and techniques, generated through business, government and university research. The requirement for genetic sequences for primer selection and validation has been greatly facilitated by the development of new sequencing techniques, machines and computer programs. Genetic libraries, such as GenBank, EMBL and DDBJ continue to accumulate a wealth of genetic sequence information for the development and validation of molecular-based diagnostic procedures concerning human and veterinary disease agents. The mechanization of various aspects of the PCR assay, such as robotics, microfluidics and nanotechnology, has made it possible for the rapid advancement of new procedures. Real-time PCR, DNA microarray and DNA chips utilize these newer techniques in conjunction with computer and computer programs. Instruments for hand-held PCR assays are being developed. The PCR and reverse transcription-PCR (RT-PCR) assays have greatly accelerated the speed and accuracy of diagnoses of human and animal disease, especially of the infectious agents that are difficult to isolate or demonstrate. The PCR has made it possible to genetically characterize a microbial isolate inexpensively and rapidly for identification, typing and epidemiological comparison.
Initial results in underwater single image dehazing (2010)

As light is transmitted from subject to observer it is absorbed and scattered by the medium it passes through. In mediums with large suspended particles, such as fog or turbid water, the effect of scattering can drastically decrease the quality of images. In this paper we present an algorithm for removing the effects of light scattering, referred to as dehazing, in underwater images. Our key contribution is to propose a simple, yet effective, prior that exploits the strong difference in attenuation between the three image color channels in water to estimate the depth of the scene. We then use this estimate to reduce the spatially varying effect of haze in the image. Our method works with a single image and does not require any specialized hardware or prior knowledge of the scene. As a by-product of the dehazing process, an up-to-scale depth map of the scene is produced. We present results over multiple real underwater images and over a controlled test set where the target distance and true colors are known.
A Rotation and a Translation Suffice: Fooling CNNs with Simple Transformations (2017)

Recent work has shown that neural network-based vision classifiers exhibit a significant vulnerability to misclassifications caused by imperceptible but adversarial perturbations of their inputs. These perturbations, however, are purely pixel-wise and built out of loss function gradients of either the attacked model or its surrogate. As a result, they tend to be contrived and look pretty artificial. This might suggest that such vulnerability to slight input perturbations can only arise in a truly adversarial setting and thus is unlikely to be an issue in more natural contexts. 
In this paper, we provide evidence that such belief might be incorrect. We demonstrate that significantly simpler, and more likely to occur naturally, transformations of the input - namely, rotations and translations alone, suffice to significantly degrade the classification performance of neural network-based vision models across a spectrum of datasets. This remains to be the case even when these models are trained using appropriate data augmentation. Finding such fooling transformations does not require having any special access to the model - just trying out a small number of random rotation and translation combinations already has a significant effect. These findings suggest that our current neural network-based vision models might not be as reliable as we tend to assume. 
Finally, we consider a new class of perturbations that combines rotations and translations with the standard pixel-wise attacks. We observe that these two types of input transformations are, in a sense, orthogonal to each other. Their effect on the performance of the model seems to be additive, while robustness to one type does not seem to affect the robustness to the other type. This suggests that this combined class of transformations is a more complete notion of similarity in the context of adversarial robustness of vision models.
Sensitive Detection of Escherichia coli O157:H7 in Food and Water by Immunomagnetic Separation and Solid-Phase Laser Cytometry (1999)

Rapid, direct methods are needed to assess active bacterial populations in water and foods. Our objective was to determine the efficiency of bacterial detection by immunomagnetic separation (IMS) and the compatibility of IMS with cyanoditolyl tetrazolium chloride (CTC) incubation to determine respiratory activity, using the pathogen Escherichia coli O157:H7. Counterstaining with a specific fluorescein-conjugated anti-O157 antibody (FAb) following CTC incubation was used to allow confirmation and visualization of bacteria by epifluorescence microscopy. Broth-grown E. coli O157:H7 was used to inoculate fresh ground beef (<17% fat), sterile 0.1% peptone, or water. Inoculated meat was diluted and homogenized in a stomacher and then incubated with paramagnetic beads coated with anti-O157 specific antibody. After IMS, cells with magnetic beads attached were stained with CTC and then an anti-O157 antibody-fluorescein isothiocyanate conjugate and filtered for microscopic enumeration or solid-phase laser cytometry. Enumeration by laser scanning permitted detection of ca. 10 CFU/g of ground beef or <10 CFU/ml of liquid sample. With inoculated meat, the regression results for log-transformed respiring FAb-positive counts of cells recovered on beads versus sorbitol-negative plate counts in the inoculum were as follows: intercept = 1.06, slope = 0.89, and r2 = 0. 95 (n = 13). The corresponding results for inoculated peptone were as follows: intercept = 0.67, slope = 0.88, and r2 = 0.98 (n = 24). Recovery of target bacteria on beads by the IMS-CTC-FAb method, compared with recovery by sorbitol MacConkey agar plating, yielded greater numbers (beef, 6.0 times; peptone, 3.0 times; water, 2.4 times). Thus, within 5 to 7 h, the IMS-CTC-FAb method detected greater numbers of E. coli O157 cells than were detected by plating. The results show that the IMS-CTC-FAb technique with enumeration by either fluorescence microscopy or solid-phase laser scanning cytometry gave results that compared favorably with plating following IMS.
Predominant Influence of Environmental Determinants on the Persistence and Avidity Maturation of Antibody Responses to Vaccines in Infants (2006)

Genetic determinants control the early phase of the vaccine antibody response in Gambian infants, whereas environmental determinants predominantly influence antibody persistence and avidity maturation.
Fen1 expression: a novel marker for cell proliferation (1998)

The identification of antigens whose expression is associated with the cell cycle is a particularly attractive method with which to define proliferative populations in histological and cytological preparations. A polyclonal antibody 3220 has been raised which recognizes the structure-specific endonuclease Fen1 and can be used for a wide range of applications including western blotting, immunoprecipitation and immunohistochemical analysis. This antibody has been used to examine Fen1 levels by immunoblotting and its subcellular localization in cultured cells and tissue samples by immunostaining. Although the role Fen1 plays in DNA replication has been well characterized, its function in DNA repair is not so clear. The possible roles of Fen1 in repair have been investigated by examining any changes in level or localization of Fen1 in response to DNA damaging agents. We find that Fen1 is a nuclear antigen, that it is expressed by cycling cells, and that it co-localizes with PCNA and polymerase alpha during S phase. Fen1 expression is topologically regulated in vivo and is associated with proliferative populations. No change has been found in either patterns or levels of Fen1 expression induced by DNA damaging agents, either in vivo or in vitro. This anti-Fen1 antiserum is well suited to the analysis of proliferation in histological material, since (1) the proportion of labelled cells equals the experimentally determined growth fraction in an experimental xenograft system and (2) unlike markers such as PCNA, Fen1 is not induced by DNA damage.
Opportunistic Mycoses in the Immunocompromised Host: Experience at a Cancer Center and Review (1992)

The field of opportunistic mycoses in the patient with cancer is rapidly changing. Not only are fungal infections increasing in frequency in this patient population, but these infections are occurring earlier during the course of cytotoxic chemotherapy, and newer fungi are increasingly recognized as potentially lethal pathogens. Candidiasis remains the most commonly encountered infection. The spectrum of disease includes candidemia and acute and chronic disseminated candidiasis. Pulmonary aspergillosis and disseminated aspergillosis are common and remain relatively resistant to therapy. Disseminated fusariosis and trichosporosis are almost always fatal in the setting of persistent profound neutropenia. Therapy for these mycoses relies on the use of amphotericin B and 5-fluorocytosine. Newer antifungal agents, such as fluconazole and itraconazole, appear to exhibit good activity against a variety of fungi. Newer approaches need to be tested for the treatment of the more-resistant mycoses and may include the use of maximally tolerated doses of antifungal agents, colony-stimulating factors, and combination therapy.
Hu23F2G, an Antibody Recognizing the Leukocyte CD11/CD18 Integrin, Reduces Injury in a Rabbit Model of Transient Focal Cerebral Ischemia (1998)

Neutrophils are known to mediate injury in acute ischemic stroke especially during reperfusion. Migration of neutrophils into regions of ischemic injury involves binding to the endothelial cell's intercellular adhesion molecule (ICAM-1) through the leukocyte integrin, CD11/CD18. We studied the potential for neuroprotection with a humanized antibody that binds to and blocks the functions of the CD11/CD18 integrin in a rabbit model of transient focal ischemia. Fifteen New Zealand White rabbits underwent transorbital occlusion of the left middle cerebral, anterior cerebral, and internal carotid arteries using aneurysm clips for 2 h, followed by 6 h of reperfusion. Treatment with a maximally saturating dose (4 mg/kg) of a humanized CD11/CD18 monoclonal antibody (Hu23F2G, ICOS Corp., Bothell, WA) (n = 8) or placebo (n = 7) was administered 20 min after occlusion and given as a single intravenous bolus. Hemispheric ischemic neuronal damage (IND) as seen on hematoxylin- and eosin-stained sections was significantly reduced in Hu23F2G-treated animals by 57% (Hu23F2G: 15 +/- 6.9%; placebo: 35 +/- 5%; mean +/- SEM, P < 0.05, t-test). Immunohistochemical staining with neutrophil elastase confirmed the presence of neutrophils within regions of IND in control brains. Treatment with Hu23F2G resulted in marked reduction of neutrophil infiltration. (No. of neutrophils/IND area: Hu23F2G 36.1 +/- 36.7 cm-2, placebo 460.6 +/- 101.8 cm-2, P = 0.001. ) Antagonism of neutrophil migration at the level of the CD11/CD18 integrin reduces ischemic injury in experimental stroke.
Growth of the coronary vasculature in hypertrophy: mechanisms and model dependence. (1994)

Coronary microvascular angiogenesis during cardiac enlargement is variable and dependent upon several factors including age, model, and duration of cardiac hypertrophy. We, and others, have documented coronary angiogenesis in several models of cardiac enlargement and in several species. Although growth of the coronary vasculature occurs during hypertension, it usually fails to compensate for the magnitude of hypertrophy. Substantial growth may occur, however, after a long period of time. In some other models of cardiac hypertrophy (excess thyroxine hormone, exercise training, and volume overload) capillary angiogenesis is greater and may occur more rapidly. An examination of a variety of models and interventions (e.g., increased myocardial perfusion, bradycardia) suggests that mechanical factors (stretch, shear stress and wall tension) associated with increases in (A) capillary perfusion, (B) diastolic interval, or (C) diastolic ventricular chamber filling may provide an initiating stimulus for capillary angiogenesis during cardiac enlargement.
Characterization of diarrheagenic Escherichia coli isolated from food in Khon Kaen, Thailand. (2005)

Four categories of 186 ready-to-eat food samples in Khon Kaen municipality, Thailand, were collected and investigated for fecal contamination by enumeration of Escherichia coli using the most probable number (MPN) method. Then, the E. coli isolates were presumptively identified as diarrheagenic E. coil by agglutinating with polyvalent O-antisera and monovalent O-antisera commonly found in diarrheagenic strains and were subsequently investigated for the presence of the recognized virulence genes for enteroaggregative (EAEC), enteroinvasive (EIEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), and shiga toxin-producing E. coli (STEC or EHEC) by multiplex PCR assays. All E, coli isolates were examined for antimicrobial susceptibilities by the agar disc diffusion method, and the results were compared with those obtained from clinical samples. The percentage of each type of food with E. coli, including no heat food, low heat food, high heat food, and fruit juices and beverages, was higher than accepted standards at 60.4, 46.5, 38.6 and 20%, respectively. Of 140 E. coli isolates obtained from food samples, 11 isolates (7.9%) agglutinated with 6 monovalent O-antisera, including one isolate each of O6, O8, O114 and O159, two isolates of O1, and five isolates of O157. None of the 11 isolates harbored the virulence genes for EPEC, ETEC, EAEC, EIEC and STEC. Although O157 E. coli isolates were found, the most frequent, E. coli O157:H7, was not found in this study. The astA gene, however, was found in 1 E. coli isolate that showed weakly positive agglutination against the polyvalent antisera. Approximately 50% of the 140 E. coli isolates were resistance to at least one antimicrobial agent. The resistant strains showed high resistance to tetracycline (43%), co-trimoxazole (36%), ampicillin (26%) and chloramphenicol (23%), respectively. The resistance of E. coli was high for nearly all antimicrobial agents, particularly ampicillin (76%), tetracycline (70%), co-trimoxazole (69%) and nalidixic acid (44%). The results show that nearly half of the ready-to-eat food samples evaluated in Khon Kaen Municipality had levels of E. coli higher than acceptable standards. Of the diarrheagenic E. coli classified by serogroup, almost none of the isolates had virulence genes. These results indicate the disadvantage of relying on serogrouping alone for the recognition of diarrheagenic E. coli. E. coli isolated from food may not be an enteropathogenic strain. We also found that E. coli antimicrobial resistant strains are widespread in both food and humans.
Lung nodule detection on thoracic computed tomography images: Preliminary evaluation of a computer‐aided diagnosis system (2002)

We are developing a computer-aided diagnosis (CAD) system for lung nodule detection on thoracic helical computed tomography (CT) images. In the first stage of this CAD system, lung regions are identified by a k-means clustering technique. Each lung slice is classified as belonging to the upper, middle, or the lower part of the lung volume. Within each lung region, structures are segmented again using weighted k-means clustering. These structures may include true lung nodules and normal structures consisting mainly of blood vessels. Rule-based classifiers are designed to distinguish nodules and normal structures using 2D and 3D features. After rule-based classification, linear discriminant analysis (LDA) is used to further reduce the number of false positive (FP) objects. We performed a preliminary study using 1454 CT slices from 34 patients with 63 lung nodules. When only LDA classification was applied to the segmented objects, the sensitivity was 84% (53/63) with 5.48 (7961/1454) FP objects per slice. When rule-based classification was used before LDA, the free response receiver operating characteristic (FROC) curve improved over the entire sensitivity and specificity ranges of interest. In particular, the FP rate decreased to 1.74 (2530/1454) objects per slice at the same sensitivity. Thus, compared to FP reduction with LDA alone, the inclusion of rule-based classification lead to an improvement in detection accuracy for the CAD system. These preliminary results demonstrate the feasibility of our approach to lung nodule detection and FP reduction on CT images.
Colloidal Carriers for Ophthalmic Drug Delivery (2005)

To achieve effective drug concentration at the intended site for a sufficient period of time is a requisite desired for many drug formulations. For drugs intended to ocular delivery, its poor bioavailability is due to pre-corneal factors. Most ocular diseases are treated by topical drug application in the form of solution, suspension and ointment. However, such dosage forms are no longer sufficient to combat some ocular diseases. Intravitreal drug injection is the current therapy for disorders in posterior segment. The procedure is associated with a high risk of complications, particularly when frequent, repeated injections are required. Thus, sustained-release technologies are being proposed, and the benefits of using colloidal carriers in intravitreal injections are currently under investigation for posterior drug delivery. This review will discuss recent progress and specific development issues relating to colloidal drug delivery systems, such as liposomes, niosomes, nanoparticles, and microemulsions in ocular drug delivery.