gebhart/patrepeval huggingface dataset:
Single Domain Antibodies: A New Concept for Epidermal Growth Factor Receptor and EGFRvIII Targeting (2012)

Epidermal growth factor receptor (EGFR) is one of the major molecular targets for cancer diagnosis and therapy. EGFR and EGFRvIII, mutated form of EGFR, have been identified as participating in pathogenesis of some forms of human cancers. Monoclonal antibodies (mAbs) targeting EGFR/EGFRvIII have been shown to suppress the signal transduction pathways controlling tumor cell growth, proliferation, and apoptosis. Until now, different types of mAbs or antibody fragments against EGFR family have been established. Some of these antibodies have been used clinically for treating various forms of human malignancies. More recently, a single domain antibody (sdAb) targeting this family of receptors has been introduced. The heavy chain antibodies (HCAbs) that made up variable regions of heavy chain, CH2, and CH3 domains are shown in camelids. SdAbs derived from camel HCAbs are the smallest known natural building parts for binding to antigen. They also possess a longer antigen recognizing region, which increases their capability for being more specific in target antigen enhancement. Camelid antibodies are highly valuable for their special characteristics, including heat resistance, small size, high solubility in an aqueous environment, and non-immunogenicity in a human environment. Due to these abilities, research on biotechnological production and treatment applications of recombinant smaller fragments of these only HCAbs is widely in progress. In this article, we will discuss the challenges and successes of different types of mAbs targeting EGFR/EGFRvIII in human cancer.
Differential Effects between γ-Secretase Inhibitors and Modulators on Cognitive Function in Amyloid Precursor Protein-Transgenic and Nontransgenic Mice (2012)

γ-Secretase inhibitors (GSIs) reduce amyloid-β (Aβ) peptides but inevitably increase the β-C-terminal fragment (β-CTF) of amyloid precursor protein (APP), potentially having undesirable effects on synapses. In contrast, γ-secretase modulators (GSMs) reduce Aβ42 without increasing β-CTF. Although the Aβ-lowering effects of these compounds have been extensively studied, little effort has been made to investigate their effects on cognition. Here, we compared the effects of two GSIs--(2S)-2-hydroxy-3-methyl-N-[(2S)-1-{[(1S)-3-methyl-2-oxo-2,3,4,5-tetrahydro-1H-3-benzazepin-1-yl]amino}-1-oxopropan-2-yl]butanamide (LY450139, semagacestat) and (2R)-2-[[(4-chlorophenyl)sulfonyl][[2-fluoro-4-(1,2,4-oxazol-3-yl)phenyl]methyl]amino-5,5,5-trifluoropentanamide (BMS-708163)--and a second-generation GSM [{(2S,4R)-1-[(4R)-1,1,1-trifluoro-7-methyloctan-4-yl]-2-[4-(trifluoromethyl)phenyl]piperidin-4-yl}acetic acid (GSM-2)] on spatial working memory in APP-transgenic (Tg2576) and nontransgenic mice using the Y-maze task. While acute dosing with either GSI ameliorated memory deficits in 5.5-month-old Tg2576 mice, these effects disappeared after 8 d subchronic dosing. Subchronic dosing with either GSI rather impaired normal cognition in 3-month-old Tg2576 mice, with no inhibition on the processing of other γ-secretase substrates, such as Notch, N-cadherin, or EphA4, in the brain. LY450139 also impaired normal cognition in wild-type mice; however, the potency was 10-fold lower than that in Tg2576 mice, indicating an APP-dependent mechanism likely with β-CTF accumulation. Immunofluorescence studies revealed that the β-CTF accumulation was localized in the presynaptic terminals of the hippocampal stratum lucidum and dentate hilus, implying an effect on presynaptic function in the mossy fibers. In contrast, both acute and subchronic dosing with GSM-2 significantly ameliorated memory deficits in Tg2576 mice and did not affect normal cognition in wild-type mice. We demonstrated a clear difference between GSI and GSM in effects on functional consequences, providing new insights into strategies for developing these drugs against Alzheimer's disease.
A Subthreshold Low-Noise Amplifier Optimized for Ultra-Low-Power Applications in the ISM Band (2008)

The IEEE 802.15.4 standard relaxes the requirements on the receiver front-end making subthreshold operation a viable solution. The specification is discussed and guidelines are presented for a small area ultra-low-power design. A subthreshold biased low-noise amplifier (LNA) has been designed and fabricated for the 2.4-GHz IEEE 802.15.4 standard using a standard low-cost 0.18-mum RF CMOS process. The single-stage LNA saves on chip area by using only one inductor. The measured gain is more than 20 dB with an S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> of -19 dB while using 630 muA of dc current. The measured noise figure is 5.2 dB.
Balancing structural hazards and hardware cost of pipelined processors (1995)

In this paper a tool to aid pipelined processor instruction set implementation is described. The purpose of the tool is to choose from among design alternatives a design that minimizes overall processor cost. In the proposed cost model, processor cost has two components, the cost of hardware necessary to realize the processor and the cost of degraded performance due to pipeline hazards as compared to an ideal pipelined processor. A previous paper detailed the optimization algorithm. This paper extends these results to handle enclosed pairs of instructions having structural hazards. The extended algorithm can produce an optimal result. This algorithm and several examples are presented. >
Smaller inner ear sensory epithelia in Neurog1 null mice are related to earlier hair cell cycle exit (2005)

We investigated whether co-expression of Neurog 1 and Atoh 1 in common neurosensory precursors could explain the loss of hair cells in Neurog 1 null mice. Analysis of terminal mitosis, using BrdU, supports previous findings regarding timing of exit from cell cycle. Specifically, we show that cell cycle exit occurs in spiral sensory neurons in a base-to-apex progression followed by cell cycle exit of hair cells in the organ of Corti in an apex-to-base progression, with some overlap of cell cycle exit in the apex for both hair cells and spiral sensory neurons. Hair cells in Neurog 1 null mice show cell cycle exit in an apex-to-base progression about 1-2 days earlier. Atoh 1 is expressed in an apex-to-base progression rather then a base-to-apex progression as in wildtype littermates. We tested the possible expression of Atoh1 in neurosensory precursors using two Atoh 1-Cre lines. We show Atoh 1-Cre mediated beta-galactosidase expression in delaminating sensory neuron precursors as well as undifferentiated epithelial cells at E11 and E12.5. PCR analysis shows expression of Atoh 1 in the otocyst as early as E10.5, prior to any histology-based detection techniques. Combined, these data suggest that low levels of Atoh 1 exist much earlier in precursors of hair cells and sensory neurons, possibly including neurosensory precursors. Analysis of Atoh 1-Cre expression in E18.5 embryos and P31 mice reveal beta-galactosidase stain in all hair cells but also in vestibular and cochlear sensory neurons and some supporting cells. A similar expression of Atoh 1-LacZ exists in postnatal and adult vestibular and cochlear sensory neurons, and Atoh 1 expression in vestibular sensory neurons is confirmed with RT-PCR. We propose that the absence of NEUROG 1 protein leads to loss of sensory neuron formation through a phenotypic switch of cycling neurosensory precursors from sensory neuron to hair cell fate. Neurog 1 null mice show a truncation of clonal expansion of hair cell precursors through temporally altered terminal mitosis, thereby resulting in smaller sensory epithelia.
Extracellular vesicles as novel carriers for therapeutic molecules (2016)

Extracellular vesicles (EVs) are natural carriers of biomolecules that play central roles in cell-to-cell communications. Based on this, there have been various attempts to use EVs as therapeutic drug carriers. From chemical reagents to nucleic acids, various macromolecules were successfully loaded into EVs; however, loading of proteins with high molecular weight has been huddled with several problems. Purification of recombinant proteins is expensive and time consuming, and easily results in modification of proteins due to physical or chemical forces. Also, the loading efficiency of conventional methods is too low for most proteins. We have recently proposed a new method, the so-called exosomes for protein loading via optically reversible protein-protein interaction (EXPLORs), to overcome the limitations. Since EXPLORs are produced by actively loading of intracellular proteins into EVs using blue light without protein purification steps, we demonstrated that the EXPLOR technique significantly improves the loading and delivery efficiency of therapeutic proteins. In further in vitro and in vivo experiments, we demonstrate the potential of EXPLOR technology as a novel platform for biopharmaceuticals, by successful delivery of several functional proteins such as Cre recombinase, into the target cells. [BMB Reports 2016; 49(11): 585-586].
The Risk of Seasonal and Pandemic Influenza: Prospects for Control (2008)

Seasonal influenza is an underappreciated cause of morbidity and mortality in the United States. Seasonal vaccination of individuals in groups at high risk of complications has long been recommended. However, there has been a gradual expansion of the recommended groups for annual influenza immunization in order to reduce the incidence of uncomplicated infection, to alleviate the impact of seasonal influenza on health care, and to simplify the application of recommendations. The threat of an influenza pandemic, heightened by recent cases of highly pathogenic avian influenza in humans, requires continued efforts in preparedness. Strategies for the control of pandemic influenza must include vaccines, antiviral drugs, and nonpharmaceutical interventions like school closure and voluntary quarantine around cases. The prophylactic efficacy of neuraminidase inhibitors, previously observed in household studies, suggests that they will be a useful adjunct to voluntary quarantine. Stockpiles of antiviral drugs are being established for therapeutic and perhaps preventive use for pandemic influenza.
Genomic instability of microsatellite repeats and its association with the evolution of chronic myelogenous leukemia [see comments] (1994)

Tumorigenesis has been shown to proceed through a series of genetic alterations involving protooncogenes and tumor-suppressor genes. Investigation of genomic instability of microsatellites has indicated a new mechanism for human carcinogenesis in hereditary nonpolyposis colorectal cancer and sporadic cancer and this instability has been shown to be related to inherited predisposition to cancer. This study was conducted to determine whether such microsatellite instability is associated with the evolution of chronic myelogenous leukemia (CML) to the blast crisis. Nineteen CML patients clinically progressing from the chronic phase to accelerated phase or blast crisis and 20 other patients in the CML chronic phase were studied. By polymerase chain reaction assay, DNAs for genomic instability in five separate microsatellites in chromosome arms 5q (Mfd27), 17p (Mfd41), 18q (DCC), 3p (CI3–9), and 8p (LPL) were examined. Differences in unrelated microsatellites of chronic and blastic phase DNAs in 14 of 19 patients (73.7%) were demonstrated. Somatic instability in five microsatellites, Mfd27, Mfd41, DCC, CI3–9, and LPL, was detected in 2 of 19 (10.5%), 8 of 19 (42.1%), 11 of 19 (57.9%), 4 of 17 (23.5%), and 4 of 17 (23.5%) cases. In 10 of 19 cases (52.6%), genetic instability in at least two of five microsatellites was observed and was categorized as replication error (RER+) phenotype. CML evolution cases with myeloid, lymphoid, and mixed phenotypes and the blast crisis and accelerated phase showed somatic instability in a number of microsatellites. No alterations in leukemic cells at the chronic phase could be detected in any microsatellites. These data indicate instability of microsatellites (RER+) but not familial predisposition to possibly be a late genetic event in the evolution of CML to blast crisis. In the microsatellite of the DCC gene, complicated alterations in band patterns caused by instability as well as loss of heterozygosity (LOH) were observed in 13 of 19 cases (68.4%): instability in 9 cases, instability plus LOH in 2 cases, and only LOH in 2 cases. These highly frequent alterations in microsatellites, including instability and LOH, suggesting that secondary events due possibly to loss of fidelity in replication and repair machinery may be significantly associated with CML evolution.
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations (2013)

Genome annotations are often published as plain text files describing genomic features and their subcomponents by an implicit annotation graph. In this paper, we present the GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation. This gives the developer intuitive and immediate access to genomic features and tools for their manipulation. To process large annotation sets with low memory overhead, we have designed and implemented an efficient pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations. Our object-oriented C-based software library enables a developer to conveniently implement their own functionality on annotation graphs and to integrate it into larger workflows, simultaneously accessing compressed sequence data if required. The careful C implementation of the GenomeTools does not only ensure a light-weight memory footprint while allowing full sequential as well as random access to the annotation graph, but also facilitates the creation of bindings to a variety of script programming languages (like Python and Ruby) sharing the same interface.
High-frequency rTMS improves time perception in Parkinson disease (2004)

Patients with Parkinson disease (PD) are impaired in time processing. The authors investigated the effects of high-frequency (5 Hz) repetitive transcranial magnetic stimulation (rTMS) in patients with PD performing a time reproduction task. The authors found significant improvement in time processing induced by rTMS when trains were applied over the right dorsolateral prefrontal cortex (DLPFC) but not over the supplementary motor area, suggesting that the circuit involving the basal ganglia and the DLPFC might constitute the neural network subserving time perception.
Influence of Tropolone on <i>Poria placenta</i> Wood Degradation (2002)

Fenton reactions are believed to play important roles in wood degradation by brown rot fungi. In this context, the effect of tropolone (2-hydroxycyclohepta-2,4,6-trienone), a metal chelator, on wood degradation by Poria placenta was investigated. Tropolone (50 micro M) strongly inhibits fungal growth on malt agar, but this inhibition could be relieved by adding iron salts. With an experimental system containing two separate parts, one supplemented with tropolone (100 micro M) and the other not, it was shown that the fungus is able to reallocate essential minerals from the area where they are available and also to grow in these conditions on malt-agar in the presence of tropolone. Nevertheless, even in the presence of an external source of metals, P. placenta is not able to attack pine blocks impregnated with tropolone (5 mM). This wood degradation inhibition is related to the presence of the tropolone hydroxyl group, as shown by the use of analogs (cyclohepta-2,4,6-trienone and 2-methoxycyclohepta-2,4,6-trienone). Furthermore, tropolone possesses both weak antioxidative and weak radical-scavenging properties and a strong affinity for ferric ion and is able to inhibit ferric iron reduction by catecholates, lowering the redox potential of the iron couple. These data are consistent with the hypothesis that tropolone inhibits wood degradation by P. placenta by chelating iron present in wood, thus avoiding initiation of the Fenton reaction. This study demonstrates that iron chelators such as tropolone could be also involved in novel and more environmentally benign preservative systems.
Bandwidth modelling for network-aware applications (1999)

Network-aware applications attempt to adjust their resource demands in response to changes in resource availability, e.g., if a server maintains a connection to a client, the server may want to adjust the amount of data sent to the client based on the effective bandwidth realized for the connection. Information about current and future network performance is therefore crucial for an adaptive application. This paper discusses three aspects of the coupling of applications and networks: (1) a network-aware application needs timely information about the status of the network; (2) a simple bandwidth estimation technique per forms reasonably well for TCP-Reno connections without timeouts; (3) enhancements proposed to TCP-Reno to reduce the number of timeouts (i.e., SACKs and its variants) increase the bandwidth but also improve the accuracy of bandwidth estimators developed by other researchers. The empirical observations reported in this paper are based on an in-vivo experiment in the Internet. Over a 6-month period, we logged the micro dynamics of random connections between a set of selected hosts. These results are encouraging for the developer of a network-aware application since they provide evidence that a simple widening of the interface between applications and network (protocol) may provide the information that allows an application to successfully adapt to changes in resource availability.
Factors affecting the stability of tPA and PAI-1 during storage and handling of human plasma for in vitro studies (1990)

Factors that influence the physico-chemical conditions of plasma (e.g. pH, dilution, freezing, storage) and thereby the stability of tPA and PAI-1 activities, have been studied and optimized using a solid-phase fibrin-tPA activity assay. Optimal recovery of tPA activity was at a pH of 6.8 +/- 0.2, while at the pHs usually found in thawed plasma, i.e. pH 7.6-8.2, the activity was lower and showed great variability. Free tPA activity was tested in undiluted plasma, while plasma diluted 1:20 was used to recover maximal tPA activity. The corrected value for the diluted plasma and the value for the euglobulin suspensions were similar. In both cases the pH optimum was 7.4. PAI activity levels were tested in undiluted plasma and showed no variations after venous occlusion. Our results indicate that the in vitro determination of tPA activity is directly related to the pH of thawed plasma and not to the freezing procedure or the temperature of storage. Therefore, thawed plasma should be tested at a pH giving the maximal recovery of tPA activity in a particular assay method.
Perioperative hypotension and myocardial ischemia: Diagnostic and therapeutic approaches (2011)

Although perioperative hypotension is a common problem, its true incidence is largely unknown. There is evidence that postoperative outcome, including the incidence of myocardial adverse events, may be linked to the prolonged episodes of perioperative hypotension. Despite this, there are very few comprehensive resources available in the literature regarding diagnosis and management of these not so uncommon clinical occurrences, especially during non-cardiac surgery. Most anesthesia providers consider intraoperative hypotension to be caused by systemic vasodilatation and relative hypovolemia and so treat it empirically. The introduction of new monitoring devices including transesophageal echocardiography and arterial pressure waveform based stroke volume measurement have provided additional tools to narrow the differential diagnoses and initiate optimal treatment measures. Understanding the basic pathophysiology of hypotension and myocardial ischemia can further assist in providing goal directed management. This article serves as a comprehensive guide for anesthesiologists to diagnose and treat hypotension and myocardial ischemia. A summary of available techniques to monitor perioperative myocardial ischemia and their limitations are also discussed.
Facile One-Pot Synthesis of 6-Monosubstituted and 6,12-Disubstituted 5,11-Dihydroindolo[3,2-<i>b</i>]carbazoles and Preparation of Various Functionalized Derivatives (2007)

A facile three-stage, one-pot approach for the synthesis of a variety of novel 6-monosubstituted and 6,12-disubstituted 5,11-dihydroindolo[3,2-b]carbazoles, in moderate to good yields (20-50%), has been developed, based on the condensation of an indole and an aldehyde with a catalytic amount of iodine, followed by an acid-catalyzed intramolecular cyclization with an ortho ester. The parent indolo[3,2-b]carbazoles (ICZs) could be converted to various functional derivatives. Both N-alkylation and N-arylation were successfully accomplished, and azo-coupling, formylation, as well as bromination were performed in a regioselective way leading to the formation of novel functional 6,12-disubstituted indolo[3,2-b]carbazoles. Starting from a monoformylated indolocarbazole, novel benzimidazolyl-substituted derivatives were synthesized, while Suzuki cross-couplings on a monobrominated building block afforded a novel pathway toward functionally arylated ICZs.
The competitive NMDA receptor antagonist CGP 40116 is a potent neuroprotectant in a rat model of focal cerebral ischemia. (1994)

Focal cerebral ischemia was induced in rats by permanent occlusion of the left middle cerebral artery (MCA). The cerebroprotective properties of the competitive NMDA antagonist CGP 40116 were evaluated in that model and compared to the neuroprotective effects of MK 801, D-CPPene and CGS 19755 under the same experimental conditions. Infarct volume was assessed using in vivo magnetic resonance imaging. The rank order of potency for the NMDA antagonists tested was MK 801 > CGP 40116 approximately D-CPPene > CGS 19755. CGP 40116 dose-dependently reduced the volume of cortical infarction, with an ED50 of 11 mg/kg i.v., and its cerebroprotective efficacy was comparable to that of MK 801. Neuroprotection by CGP 40116 was still apparent when treatment was started 30 minutes after MCA occlusion. It is concluded that CGP 40116 is an effective cerebroprotectant with potential clinical utility for amelioration of focal cerebral ischemic damage.