gebhart/patrepeval huggingface dataset:
The Atg16L Complex Specifies the Site of LC3 Lipidation for Membrane Biogenesis in Autophagy (2008)

Two ubiquitin-like molecules, Atg12 and LC3/Atg8, are involved in autophagosome biogenesis. Atg12 is conjugated to Atg5 and forms an approximately 800-kDa protein complex with Atg16L (referred to as Atg16L complex). LC3/Atg8 is conjugated to phosphatidylethanolamine and is associated with autophagosome formation, perhaps by enabling membrane elongation. Although the Atg16L complex is required for efficient LC3 lipidation, its role is unknown. Here, we show that overexpression of Atg12 or Atg16L inhibits autophagosome formation. Mechanistically, the site of LC3 lipidation is determined by the membrane localization of the Atg16L complex as well as the interaction of Atg12 with Atg3, the E2 enzyme for the LC3 lipidation process. Forced localization of Atg16L to the plasma membrane enabled ectopic LC3 lipidation at that site. We propose that the Atg16L complex is a new type of E3-like enzyme that functions as a scaffold for LC3 lipidation by dynamically localizing to the putative source membranes for autophagosome formation.
[TPX2 expression and its significance in squamous cell carcinoma of lung]. (2006)

To study the expression of targeting protein for Xklp2 (TPX2) and its significance in squamous cell carcinoma (SCC) of the lung.Two SCC cell lines and 4 immortalized bronchial epithelial cell lines (as a precancerous model) were examined by Western blot for TPX2 expression. Reverse transcription-polymerase chain reaction analysis for TPX2 was also performed using tumor tissues from 21 patients with SCC of the lung. The expression of TPX2 was studied by immunohistochemistry (using tissue microarray) on paraffin-embedded sections of pulmonary SCC and corresponding precancerous lesions from a group of 319 patients.TPX2 was variably expressed in all the cell lines studied. Compared with matched controls using normal lung tissue, high level of TPX2 mRNA was detected in 16 of the 21 SCC tumor tissue samples analyzed. Immunohistochemical study showed that TPX2 was mainly present in tumor tissues but not in normal controls. The expression of TPX2 correlated with tumor grade, stage and nodal status. As for precancerous lesions, the level of TPX2 was also increased, in accordance with the degree of dysplasia.Expression of TPX2 may play a role in carcinogenesis of bronchial epithelium and tumor progression of pulmonary SCC. It may also represent a potential biomarker for surveillance of SCC of lung.
The pathophysiological basis of acute‐on‐chronic liver failure (2002)

The vast majority of patients that are referred to a specialist hepatological centre suffer from acute deterioration of their chronic liver disease. Yet, this entity of acute-on-chronic liver failure remains poorly defined. With the emergence of newer liver support strategies, it has become necessary to define this entity, its pathophysiology and the short and long-term prognosis. This review focuses upon how a precipitant such as an episode of gastrointestinal bleeding or sepsis may start a cascade of events that culminate in end-organ dysfunction and liver failure. We briefly review the pathophysiological basis of the therapeutic modalities that are available. Our current strategy for the management of liver failure involves supportive therapy for the end-organs with the hope that the liver function would recover if sufficient time for such a recovery is allowed. Because liver failure, whether of the acute or acute-on-chronic variety, is potentially reversible, the stage is set for the application of newer liver support strategies to enhance the recovery process.
A High Yielding Chemical Synthesis of Sialyl Lewis x Tetrasaccharide and Lewis x Trisaccharide; Examples of Regio- and Stereodifferentiated Glycosylations (1998)

Virtually complete regioselective galactosylation of the diol acceptor p-methoxyphenyl 6-O-benzyl-2-deoxy-2-tetrachlorophthalimido-β-d-glucopyranoside (8) with the donor phenyl 2,3,4-tri-O-acetyl-6-O-benzyl-1-thio-β-d-galactopyranoside (11) gave the lactosamine derivative 14, which was fucosylated with the donor 15 to give the Lex trisaccharide glycoside 2 after deprotection. Regioselective sialylation of the partially protected Lex trisaccharide triol 24 with the sialyl donor 25 gave, after deprotection, the SLex tetrasaccharide glycoside 1. The overall yields of 2 and 1 from the monosaccharide starting materials 8, 11, 15, and 25 were 56% and 29%, respectively. In contrast to the virtually complete regio- and stereoselective galactosylation of 8, fucosylation with the benzyl-protected donor 15 gave the corresponding 1→3- and 1→4-linked disaccharides in a ratio of 3.6:1 (highly stereo- but not regioselective glycosylation), whereas fucosylation with acetyl-protected donor 18 gave a 2.2:1 β/α-mixture of 4-O-linked disaccharides (highly regio- but not stereoselective glycosylation).
Direct observation of 1-azafulven-6-one and annelated derivatives (1982)

1-Azafulven-6-one, 2-carbonyl-2H-indole, 5-carbonyl-5H-furo[3,2-b]pyrrole, and thieno- and pyrrolo-analogues are isolated at low temperatures following thermal elimination of water or methanol from the corresponding carboxylic acids or esters; the azafulvenones dimerise at –100 to –40 °C to diketopiperazine derivatives.
Antibodies against Mac-1 Attenuate Neutrophil Accumulation after Traumatic Brain Injury in Rats (1996)

Neutrophils (PMN) accumulate and are associated with cerebrovascular disturbances after experimental traumatic or ischemic brain injury, and meningitis. We hypothesized that posttraumatic PMN accumulation in brain is mediated by the PMN adhesion receptor Mac-1 (CD11b/CD18). Anesthetized rats were randomized to receive 2 mg/kg intravenously of murine monoclonal antibody to rat Mac-1 (1-B6) or anti-Mac-1 F(ab)2' [1-B6F(ab)2'] fragment (Repligen Corp., Cambridge, MA). Control rats were treated with isotype matched control antibody. Rats were subjected to percussive trauma to the right parietal cortex 30 min after treatment. Rats were killed 24 h posttrauma, and PMN accumulation was assessed by myeloperoxidase (MPO) activity. The presence of 1-B6F(ab)2' bound to PMN in brain after trauma was assessed by immunohistochemistry. Complete blood cell counts were obtained before treatment and 24 h after trauma. Brain MPO activity was reduced by 43% in the 1-B6-treated rats vs. controls (0.31 +/- 0.09 vs 0.55 +/- 0.10 U/g, n = 6/group, p = 0.013) and by 34% in the 1-B6F(ab)2'-treated rats vs. controls (0.43 +/- 0.10 vs. 0.65 +/- 0.09 U/g, n = 6/group, p = 0.006). Systemic neutropenia developed in the 1-B6-treated rats (absolute PMN count decreased by 73% vs. baseline) but not in rats treated with 1-B6F(ab)2' (absolute PMN count increased by 26 and 25% vs. baseline in treated and controls, respectively). Immunohistochemical staining showed 1-B6F(ab)2' on the surface of infiltrated PMN 24 h after trauma. Mac-1 mediates posttraumatic PMN accumulation in brain. This accumulation can be attenuated by 34%, without reducing circulating PMN, using an anti-Mac-1 F(ab)2' fragment; however, some PMN coated with 1-B6F(ab)2' still infiltrate into traumatized tissue. These results are similar to those reported in models of cerebral ischemia, and suggest the participation of multiple PMN adhesion pathways after ischemic and traumatic brain injury.
Current Status of Augmentation and Combination Treatments for Major Depressive Disorder: A Literature Review and a Proposal for a Novel Approach to Improve Practice (2006)

Most patients with major depressive disorder (MDD) do not reach symptom remission. These patients with residual symptoms have worse function and worse prognosis than those who remit. Several augmentation and combination treatments are used to either increase the chances of achieving remission or to eliminate/minimize residual depressive symptoms. Evidence for these pharmacological approaches rests primarily on open, uncontrolled studies, and there are clearly not enough controlled studies. Clinicians should carefully weigh these different treatment options to increase their patients' chances of achieving and sustaining remission from depression. This paper will review the pertinent studies and will propose a novel approach to improve practice involving the use of augmentation or combination strategies at the outset of initial treatment to primarily enhance the chances of remission through synergy and/or a broader spectrum of action. This novel approach could potentially enhance retention and/or increase remission rates since the lack of response with antidepressant monotherapy may lead many depressed patients with little or no benefit to drop out of treatment, precluding the subsequent use of augmentation or combination strategies altogether. In addition, the emergence of certain side-effects (e.g., agitation, insomnia) or the persistence of some initial baseline symptoms (e.g., anxiety, insomnia) may lead to premature discontinuation from monotherapy in the absence of concomitant use of augmenting pharmacological options targeting these symptoms.
Modified proenzymes as artificial substrates for proteolytic enzymes: colorimetric assay of bacterial collagenase and matrix metalloproteinase activity using modified pro-urokinase (1997)

We describe a new principle for assessment of the activity of proteolytic enzymes of all classes and show the application of this principle for the quantitative assay of bacterial collagenase and human matrix metalloproteinases (MMPs). Central to this new principle is the presence of a proenzyme that can be activated into an active enzyme by a single proteolytic event. The regular activation sequence in the proenzyme is replaced using protein engineering by an artificial sequence recognized by the proteinase to be determined. The latter can act as an activator for the newly engineered proenzyme. In the present paper a simple colorimetric assay for the determination for MMPs is described based on this principle. With the aid of protein engineering, a modified pro-urokinase has been prepared in which the activation sequence normally recognized by plasmin (Pro-Arg-Phe-Lys upward arrowIle-Ile-Gly-Gly) has been replaced by a sequence expected to be recognized and hydrolysed by many MMPs (Arg-Pro-Leu-Gly upward arrowIle-Ile-Gly-Gly). The active urokinase resulting from activation of the modified pro-urokinase by a MMP could be measured either directly, using a specific chromogenic peptide substrate for urokinase, or indirectly via urokinase-catalysed plasminogen activation. The response of the assay to equal molar quantities of active MMPs decreases in the order MMP-2>MMP-9>MMP-1>MMP-3>MMP-7. The detection limit for MMP-9 was below 15 pM, corresponding to 3. 75x10(-15) mol per assay. Using the assay, increased MMP activity was detected in synovial tissue extracts from rheumatoid arthritis patients compared with those from osteoarthritis patients, and in stomach tumour extracts as compared with normal stomach tissue extracts.
2'-Deoxy-2'-methylenecytidine and 2'-deoxy-2',2'-difluorocytidine 5'-diphosphates: potent mechanism-based inhibitors of ribonucleotide reductase (1991)

It has been found that 2'-deoxy-2'-methyleneuridine (MdUrd), 2'-deoxy-2'-methylenecytidine (MdCyd), and 2'-deoxy-2',2'-difluorocytidine (dFdCyd) 5'-diphosphates (MdUDP (1) MdCDP (2) and dFdCDP (3), respectively) function as irreversible inactivators of the Escherichia coli ribonucleoside diphosphate reductase (RDPR). 2 is a much more potent inhibitor than its uridine analogue 1. It is proposed that 2 undergoes abstraction of H3' to give an allylic radical that captures a hydrogen atom and decomposes to an active alkylating furanone species. RDPR also accepts 3 as an alternative substrate analogue and presumably executes an initial abstraction of H3' to initiate formation of a suicide species. Both 2 and 3 give inactivation results that differ from those of previously studied inhibitors. The potent anticancer activities of MdCyd and dFdCyd indicate a significant chemotherapeutic potential. The analogous RDPR of mammalian cells should be regarded as a likely target and/or activating enzyme for these novel mechanism-based inactivators.
The effect of abdominal wall morphology on ultrasonic pulse distortion. Part I. Measurements (1998)

The relative importance of the fat and muscle layers of the human abdominal wall in producing ultrasonic wavefront distortion was assessed by means of direct measurements. Specimens employed included six whole abdominal wall specimens and twelve partial specimens obtained by dividing each whole specimen into a fat and a muscle layer. In the measurement technique employed, a hemispheric transducer transmitted a 3.75-MHz ultrasonic pulse through a tissue section. The received wavefront was measured by a linear array translated in the elevation direction to synthesize a two-dimensional aperture. Insertion loss was also measured at various locations on each specimen. Differences in arrival time and energy level between the measured waveforms and computed references that account for geometric delay and spreading were calculated. After correction for the effects of geometry, the received waveforms were synthetically focused. The characteristics of the distortion produced by each specimen and the quality of the resulting focus were analyzed and compared. The measurements show that muscle produces greater arrival time distortion than fat while fat produces greater energy level distortion than muscle, but that the distortion produced by the entire abdominal wall is not equivalent to a simple combination of distortion effects produced by the layers. The results also indicate that both fat and muscle layers contribute significantly to the distortion of ultrasonic beams by the abdominal wall. However, the spatial characteristics of the distortion produced by fat and muscle layers differ substantially. Distortion produced by muscle layers, as well as focal images aberrated by muscle layers, show considerable anisotropy associated with muscle fiber orientation. Distortion produced by fat layers shows smaller-scale, granular structure associated with scattering from the septa surrounding individual fat lobules. Thick layers of fat may be expected to cause poor image quality due to both scattering and bulk absorption effects, while thick muscle layers may be expected to cause focus aberration due to large arrival time fluctuations. Correction of aberrated focuses using time-shift compensation shows more complete correction for muscle sections than for fat sections, so that correction methods based on phase screen models may be more appropriate for muscle layers than for fat layers.
Unexplained infertility: a review of diagnosis, prognosis, treatment efficacy and management (1992)

The dilemma of unexplained infertility posed by Southam in 1960 remains today: despite advances in the diagnostic assessment of infertility, many couples still have no explanation for their infertility. Even the most sophisticated evaluation of semen, ovulation and genital tract competence cannot reveal all of the possible defects in the complex process leading to conception. Because it arises from these shortcomings in our knowledge of fertilization and from our inability to utilize all of the current knowledge, unexplained infertility is a challenge for both biological and clinical research. This paper attempts to summarize some clinical issues in the management of unexplained infertility: the prevalence of the disorder, problems in the definition and possible explanations for the existence of this diagnostic category. It reviews outcome-based clinical publications as a guide to decision-making on what diagnostic tests to use, provides a summary of the untreated prognosis and evaluates study results that may serve as a basis for treatment decisions in this puzzling diagnostic category of infertility.
Tissue Transglutaminase Activation Modulates Inflammation in Cystic Fibrosis via PPARγ Down-Regulation (2008)

Cystic fibrosis (CF), the most common life-threatening inherited disease in Caucasians, is due to mutations in the CF transmembrane conductance regulator (CFTR) gene and is characterized by airways chronic inflammation and pulmonary infections. The inflammatory response is not secondary to the pulmonary infections. Indeed, several studies have shown an increased proinflammatory activity in the CF tissues, regardless of bacterial infections, because inflammation is similarly observed in CFTR-defective cell lines kept in sterile conditions. Despite recent studies that have indicated that CF airway epithelial cells can spontaneously initiate the inflammatory cascade, we still do not have a clear insight of the molecular mechanisms involved in this increased inflammatory response. In this study, to understand these mechanisms, we investigated ex vivo cultures of nasal polyp mucosal explants of CF patients and controls, CFTR-defective IB3-1 bronchial epithelial cells, C38 isogenic CFTR corrected, and 16HBE normal bronchial epithelial cell lines. We have shown that a defective CFTR induces a remarkable up-regulation of tissue transglutaminase (TG2) in both tissues and cell lines. The increased TG2 activity leads to functional sequestration of the anti-inflammatory peroxisome proliferator-activated receptor gamma and increase of the classic parameters of inflammation, such as TNF-alpha, tyrosine phosphorylation, and MAPKs. Specific inhibition of TG2 was able to reinstate normal levels of peroxisome proliferator-activated receptor-gamma and dampen down inflammation both in CF tissues and CFTR-defective cells. Our results highlight an unpredicted central role of TG2 in the mechanistic pathway of CF inflammation, also opening a possible new wave of therapies for sufferers of chronic inflammatory diseases.
Subretinal transplantation of genetically modified human cell lines attenuates loss of visual function in dystrophic rats (2001)

Royal College of Surgeons rats are genetically predisposed to undergo significant visual loss caused by a primary dysfunction of retinal pigment epithelial (RPE) cells. By using this model, we have examined the efficacy of subretinal transplantation of two independent human RPE cell lines each exhibiting genetic modifications that confer long-term stability in vitro. The two cell lines, a spontaneously derived cell line (ARPE19) and an extensively characterized genetically engineered human RPE cell line (h1RPE7), which expresses SV40 large T (tumor) antigen, were evaluated separately. Both lines result in a significant preservation of visual function as assessed by either behavioral or physiological techniques. This attenuation of visual loss correlates with photoreceptor survival and the presence of donor cells in the areas of rescued photoreceptors at 5 months postgrafting (6 months of age). These results demonstrate the potential of genetically modified human RPE cells for ultimate application in therapeutic transplantation strategies for retinal degenerative diseases caused by RPE dysfunction.
The pre‐synaptic motor nerve terminal as a site for antibody‐mediated neurotoxicity in autoimmune neuropathies and synaptopathies (2013)

The pre-synaptic motor nerve terminal is a highly complex and dynamic compartment within the lower motor neuron responsible for converting electrical signals into secreted chemicals. This self-renewing process of synaptic transmission is accomplished by the calcium-triggered fusion of neurotransmitter-containing vesicles with the plasma membrane and the subsequent retrieval and recycling of vesicle components. Besides this conventional physiological role, the highly active process of vesicle fusion and re-uptake into endosomal sorting pathways acts as a conduit for entry of a range of substances into the intracellular compartment of the motor nerve terminal. Whilst this entry portal sub-serves many vital physiological processes, such as those mediated by neurotrophin trafficking, there is also the potential for substantial pathological consequences resulting from uptake of noxious agents, including autoantibodies, viruses and toxins. These may act locally to induce disease within the nerve terminal, or traffic beyond to the motor neuron cell body and central nervous system to exert their pathological effects. This review focuses on the recent evidence that the ganglioside-rich pre-synaptic membrane acts as a binding site for potentially neurotoxic serum autoantibodies that are present in human autoimmune motor neuropathies. Autoantibodies that bind surface antigens induce membrane lytic effects, whereas their uptake attenuates local injury and transfers any potential pathological consequences to the intracellular compartment. Herein the thesis is explored that a balance exists between local injury at the exofacial leaflet of the pre-synaptic membrane and antibody uptake, which dictates the overall level and site of motor nerve injury in this group of disorders.
Monoclonal antibody against human T cell leukemia virus p19 defines a human thymic epithelial antigen acquired during ontogeny. (1983)

Using monoclonal antibody 12/1-2 against a 19,000-dalton human T cell leukemia virus (HTLV) protein (anti-p19), previously demonstrated to be reactive with HTLV-infected human cells, but not in numerous other uninfected cells, we found a reactive antigen to be expressed on the neuroendocrine component of human thymic epithelial cells but not on any other normal epithelial or neuroendocrine human tissues. Moreover, this reactive antigen is acquired on neuroendocrine thymic epithelium during thymic ontogeny--first appearing on fetal thymic epithelial cells between 8 and 15 wk gestation. While only a portion of thymic epithelial cells in the subcapsular cortical region of 15- and 24-wk fetal thymuses contained anti-p19+ epithelial cells, the entire subcapsular cortical region of newborn thymus epithelium was anti-p19+. By age 3 yr, normal subjects' entire subcapsular cortical and medullary thymic epithelium was anti-p19+. Using antibody against HTLV core protein, p24, and c-DNA probes for HTLV DNA, neither HTLV-specific p24 protein nor proviral DNA could be demonstrated in anti-p19+ thymic epithelial tissue. However, thymic epithelial extracts, disrupted HTLV extracts, as well as purified HTLV p19 antigen all inhibited the binding of anti-p19 antibody to thymic epithelium. Thus, anti-p19 may recognize a determinant on an HTLV-encoded 19,000-dalton structural protein that is shared by human thymic epithelium. Alternatively, anti-p19 defines a host encoded protein that is selectively expressed by normal thymic epithelium, and is induced to be expressed in HTLV-infected malignant T cells.
A Comparison of Omeprazole with Ranitidine for Ulcers Associated with Nonsteroidal Antiinflammatory Drugs (1998)

In patients with regular use of NSAIDs, omeprazole healed and prevented ulcers more effectively than did ranitidine.
Prevention of Type 2 Diabetes Mellitus by Changes in Lifestyle among Subjects with Impaired Glucose Tolerance (2001)

Type 2 diabetes can be prevented by changes in the lifestyles of high-risk subjects.