gebhart/patrepeval huggingface dataset:
A Large-Scale Analysis of Odor Coding in the Olfactory Epithelium (2011)

Mammals can perceive and discriminate myriad volatile chemicals as having a distinct odor. Odorants are initially detected by odorant receptors (ORs) on olfactory sensory neurons (OSNs) in the nose. In the mouse, each OSN expresses one of ∼1000 different OR genes. Although OSNs and their expressed ORs constitute the fundamental units of sensory input to the brain, a comprehensive understanding of how they encode odor identities is still lacking. To gain a broader and more detailed understanding of odorant recognition and odor coding at this level, we tested the responses of 3000 mouse OSNs to 125 odorants with diverse structures and perceived odors. These studies revealed extraordinary diversity, but also bias, in odorant recognition by the OSN, and thus OR, repertoire. They indicate that most OSNs are narrowly tuned to detect a subset of odorants with related structures and often related odors, but that the repertoire also includes broadly tuned components. Strikingly, the vast majority of odorants activated a unique set of OSNs, usually two or more in combination. The resulting combinatorial codes varied in size among odorants and sometimes contained both narrowly and broadly tuned components. While many OSNs recognized multiple odorants, some appeared specific for a given pheromone or other animal-associated compound, or for one or more odorants with a particular odor quality, raising the possibility that signals derived from some OSNs and ORs might elicit an innate behavior or convey a specific odor quality.
Intracellularly Degradable Polyelectrolyte Microcapsules (2006)

Intracellular uptake and degradation of polyelectrolyte capsules is reported in this work. Two types of intracellular degradable capsules are described: enzyme-sensitive and hydrolysis- sensitive capsules (see figure). The results may be a significant step towards the biomedical application of polyelectrolyte capsules.
Coexpression profile of leukemic stem cell markers for combinatorial targeted therapy in AML (2018)

Targeted immunotherapy in acute myeloid leukemia (AML) is challenged by the lack of AML-specific target antigens and clonal heterogeneity, leading to unwanted on-target off-leukemia toxicity and risk of relapse from minor clones. We hypothesize that combinatorial targeting of AML cells can enhance therapeutic efficacy without increasing toxicity. To identify target antigen combinations specific for AML and leukemic stem cells, we generated a detailed protein expression profile based on flow cytometry of primary AML (n = 356) and normal bone marrow samples (n = 34), and a recently reported integrated normal tissue proteomic data set. We analyzed antigen expression levels of CD33, CD123, CLL1, TIM3, CD244 and CD7 on AML bulk and leukemic stem cells at initial diagnosis (n = 302) and relapse (n = 54). CD33, CD123, CLL1, TIM3 and CD244 were ubiquitously expressed on AML bulk cells at initial diagnosis and relapse, irrespective of genetic characteristics. For each analyzed target, we found additional expression in different populations of normal hematopoiesis. Analyzing the coexpression of our six targets in all dual combinations (n = 15), we found CD33/TIM3 and CLL1/TIM3 to be highly positive in AML compared with normal hematopoiesis and non-hematopoietic tissues. Our findings indicate that combinatorial targeting of CD33/TIM3 or CLL1/TIM3 may enhance therapeutic efficacy without aggravating toxicity in immunotherapy of AML.
Distribution and metabolism in healthy volunteers of disodium azodisalicylate, a potential therapeutic agent for ulcerative colitis. (1982)

A series of experiments has been performed in healthy male volunteers to investigate the disposition of orally administered disodium azodisalicylate, a potentially useful drug for the treatment of ulcerative colitis. The drug was given by mouth in doses of up to 2 g a day for six weeks and there were no adverse effects. Serum concentrations of the intact compound were low and the serum half-time was 4-12.8 days, probably because of a combination of a low clearance rate and a high apparent volume of distribution. Less than 5% of the ingested dose was excreted unchanged in the urine. Circulating concentrations of 5-ASA and N-acetyl-5-ASA were low and 30% of the equivalent daily dose was excreted in the urine, predominantly as N-acetyl-5-ASA. In most subjects more than 30% of the equivalent daily dose of 5-ASA was recovered from the faeces, either as 5-ASA itself or as the acetylated derivative. As 5-ASA has been shown to be the active therapeutic moiety of sulphasalazine, disodium azodisalicylate appears to be suitable for therapeutic trial in ulcerative colitis.
Suppression of paroxysmal atrial fibrillation by pacing. (2003)

Atrial Fibrillation (AF) affects approximately five million people world- wide. The incidence of AF increases with aging and more common in males.1 Atrial fibrillation is the most common cardiogenic cause of stroke and exacerbates heart failure. Despite the prevalence of AF, it is still one of the most difficult arrhythmia to treat.2 The management option of AF ranges from pharmacological therapy, catheter based ablation and surgery. However, non-traditional uses of pacemaker therapy have been reported in recent past.
 Pacing therapies for AF are specific to the nature of the patient’s AF. 3,4 Pharmacological management alone is the typical initial course of action. In AF cases where rapid ventricular rates cannot be controlled by pharmacological therapy, ventricular pacing therapy may be combined with radiofrequency catheter ablation of AV node. 5
Gutted Adenoviral Vectors for Gene Transfer to Muscle (2003)

Adenoviral vectors are a popular choice for gene transfer protocols because they are well characterized, have a relatively large cloning capacity (up to 36 kB), and can be grown to high titers (1013 particles/mL) (). Despite these attributes, first-generation adenoviral vectors retain many viral genes that can elicit a strong immune response, severely limiting their utility for studies in vivo (). Our laboratory and others have been developing “gutted” or helper-dependent adenoviruses, which lack all viral coding sequences and therefore should greatly enhance the persistence of the vector in vivo (,). We have used this technology to deliver to muscle full-length cDNAs of the largest known gene, dystrophin, under control of the mouse muscle creatine kinase enhancer plus promoter (, , ).
CoPub: a literature-based keyword enrichment tool for microarray data analysis (2008)

Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl.
UIMA: an architectural approach to unstructured information processing in the corporate research environment (2004)

IBM Research has over 200 people working on Unstructured Information Management (UIM) technologies with a strong focus on Natural Language Processing (NLP). These researchers are engaged in activities ranging from natural language dialog, information retrieval, topic-tracking, named-entity detection, document classification and machine translation to bioinformatics and open-domain question answering. An analysis of these activities strongly suggested that improving the organization's ability to quickly discover each other's results and rapidly combine different technologies and approaches would accelerate scientific advance. Furthermore, the ability to reuse and combine results through a common architecture and a robust software framework would accelerate the transfer of research results in NLP into IBM's product platforms. Market analyses indicating a growing need to process unstructured information, specifically multilingual, natural language text, coupled with IBM Research's investment in NLP, led to the development of middleware architecture for processing unstructured information dubbed UIMA. At the heart of UIMA are powerful search capabilities and a data-driven framework for the development, composition and distributed deployment of analysis engines . In this paper we give a general introduction to UIMA focusing on the design points of its analysis engine architecture and we discuss how UIMA is helping to accelerate research and technology transfer.
Towards Neuronal Organoids: A Method for Long-Term Culturing of High-Density Hippocampal Neurons (2013)

One of the goals in neuroscience is to obtain tractable laboratory cultures that closely recapitulate in vivo systems while still providing ease of use in the lab. Because neurons can exist in the body over a lifetime, long-term culture systems are necessary so as to closely mimic the physiological conditions under laboratory culture conditions. Ideally, such a neuronal organoid culture would contain multiple cell types, be highly differentiated, and have a high density of interconnected cells. However, before these types of cultures can be created, certain problems associated with long-term neuronal culturing must be addressed. We sought to develop a new protocol which may further prolong the duration and integrity of E18 rat hippocampal cultures. We have developed a protocol that allows for culturing of E18 hippocampal neurons at high densities for more than 120 days. These cultured hippocampal neurons are (i) well differentiated with high numbers of synapses, (ii) anchored securely to their substrate, (iii) have high levels of functional connectivity, and (iv) form dense multilayered cellular networks. We propose that our culture methodology is likely to be effective for multiple neuronal subtypesparticularly those that can be grown in Neurobasal/B27 media. This methodology presents new avenues for long-term functional studies in neurons.
A Reusable Flow-Through Polymerase Chain Reaction Instrument for the Continuous Monitoring of Infectious Biological Agents (2003)

Continuous monitoring of the environment for infectious diseases and related biowarfare agents requires the implementation of practical cost-effective methodologies that are highly sensitive and specific. One compatible method employed in clinical diagnostics is real-time polymerase chain reaction (PCR) analysis. The utility of this technique for environmental monitoring is limited, however, by the utilization of single-use consumables in commercial PCR instruments. This greatly increases mechanical complexity, because sophisticated robotic mechanisms must replenish the disposable elements. An alternative strategy develops an autonomous monitoring system consisting of reusable modules that readily interface with fluidic circuitry in a flow-through scheme. The reduced complexity should increase reliability while decreasing operating costs. In this report, we describe a reusable, flow-through PCR module that functions as one component in such a system. This module was rigorously evaluated with Bacillus anthracis genomic DNA and demonstrated high repeatability, sensitivity, and efficiency, with no evidence of sample-to-sample carryover.
A Low-Power Deep Neural Network Online Learning Processor for Real-Time Object Tracking Application (2018)

A deep neural network (DNN) online learning processor is proposed with high throughput and low power consumption to achieve real-time object tracking in mobile devices. Four key features enable a low-power DNN online learning. First, a proposed processor is designed with a unified core architecture and it achieves 1.33× higher throughput than the previous state-of-the-art DNN learning processor. Second, the new algorithms, binary feedback alignment (BFA), and dynamic fixed-point based run-length compression (RLC), are proposed and reduce power consumption through the reduction of external memory accesses (EMA). The BFA and dynamic fixed-point-based RLC reduce the EMA by 11.4% and 32.5%, respectively. Third, the new data feeding units, including an integral RLC (iRLC) decoder and a transpose RLC (tRLC) decoder, are co-designed to maximize throughput alongside the proposed algorithms. Finally, a dropout controller in this processor reduces redundant power consumption coming from the unified core and the data feeding architecture by the proposed dynamic clock-gating scheme. This enables the proposed processor to operate DNN online learning with 38.1% lower power consumption. Implemented with 65 nm CMOS technology, the 3.52 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> DNN online learning processor shows 126 mW power consumption and the processor achieves 30.4 frames-per-second throughput in the object tracking application.
Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene (2007)

Successful PCR starts with proper priming between an oligonucleotide primer and the template DNA. However, the inevitable risk of mismatched priming cannot be avoided in the currently used primer system, even though considerable time and effort are devoted to primer design and optimization of reaction conditions. Here, we report a novel dual priming oligonucleotide (DPO) which contains two separate priming regions joined by a polydeoxyinosine linker. The linker assumes a bubble-like structure which itself is not involved in priming, but rather delineates the boundary between the two parts of the primer. This structure results in two primer segments with distinct annealing properties: a longer 5'-segment that initiates stable priming, and a short 3'-segment that determines target-specific extension. This DPO-based system is a fundamental tool for blocking extension of non-specifically primed templates, and thereby generates consistently high PCR specificity even under less than optimal PCR conditions. The strength and utility of the DPO system are demonstrated here using multiplex PCR and SNP genotyping PCR.
A novel tunable filter enabling both center frequency and bandwidth tunability (2012)

This paper presents a novel filter circuit configuration that enables both the center frequency and the bandwidth to be tuned with a steep frequency response. Digital-type and microelectromechanical system (MEMS) analog-type tunable filters with a small size of 3.3 mm × 3.8 mm on a high-k low-temperature-co-fired-ceramics (LTCC) wiring wafer have been developed to verify the proposed filter configuration. The digital type achieved a wide tuning range of 62.7% from 1.4GHz to 2.7 GHz with an insertion loss of 2.21 – 2.48 dB. And a 119% bandwidth tuning from 300 MHz to 650 MHz was also verified with an insertion loss under −3dB. Moreover, the analog type achieved a center frequency tuning about 600 MHz from 2.8 GHz to 3.4 GHz using integrated MEMS varactors. The new filter configuration was verified to enable a steep frequency response with a shape factor less than 2.
Modulation of hepcidin to treat iron deregulation: potential clinical applications (2015)

The secreted peptide hormone hepcidin regulates systemic and local iron homeostasis through degradation of the iron exporter ferroportin. Dysregulation of hepcidin leads to altered iron homeostasis and development of pathological disorders including hemochromatosis, and iron loading and iron restrictive anemias. Therapeutic modulation of hepcidin is a promising method to ameliorate these conditions. Several approaches have been taken to enhance or reduce the effects of hepcidin in vitro and in vivo. Based on these approaches, hepcidin modulating drugs have been developed and are undergoing clinical evaluation. In this article we review the rationale for development of these drugs, the data concerning their safety and efficacy, their therapeutic uses, and potential future prospects.
Thrombus Precursor Protein and the measurement of thrombosis in patients with acute chest pain syndrome. (1998)

The major limitation of current diagnostic methods for the rapid diagnosis of an acute myocardial infarction (AMI) involves the measurement of the effects of ischemic or necrotic processes on myocardial function rather than the detection of the precipitating thrombotic event. The utility of an assay was investigated for thrombus precursor protein (TpP) in the diagnosis of 115 patients with symptoms consistent with myocardial ischemia or infarction of less than six hours in duration. Samples from patients were drawn at 0, 1, 2, 4, 8, 16, and 24 hours post presentation, and creatine kinase, CK-MB, myoglobin, troponin I, and TpP concentrations were determined. Significantly abnormal concentrations of TpP were observed in 15 of 17 patients presenting with an AMI within 6 hours of the onset of symptoms (p < 0.00001), 2 of 8 patients presenting with an AMI after 6 hours from the onset of symptoms (p = 0.0077), 22 of 35 patients with unstable angina (p = 0.00035), 15 of 30 patients with angina (p = 0.00024), 3 of 5 patients with atrial fibrillation (P = 0.00005), 6 of 9 patients with congestive heart failure (p = 0.00002), and 6 of 11 patients with non-cardiac chest pain (p = 0.00139). Non-cardiac chest pain patients with gastroenteritis, esophageal spasm, duodenal ulcer, cocaine overdose, and pericarditis presented with abnormal plasma concentrations of thrombus precursor protein. Peak concentrations of TpP in patients with AMI preceded those of the other markers by two to four hours.
Tuning Substrate Surface Energies for Blends of Polystyrene and Poly(methyl methacrylate) (2003)

We compare the efficacies of three preparation methods intended to create in an easy and inexpensive way a nonpreferential surface for a two-component homopolymer blend of polystyrene and poly(methyl methacrylate). The first method is to physically absorb two different high molecular weight copolymers of styrene and methyl methacrylate onto hydroxylated silicon oxide. The second method consists of covalently bonding octyltrichlorosilane onto hydroxylated silicon oxide with gradient coverage to create a region with a neutral surface. The third method utilizes hydroxyl terminated, miscible, low molecular weight homopolymers of polystyrene and poly(methyl methacrylate) covalently attached to the substrate. We characterize the relative effectiveness of all three methods and their temporal stability using optical microscopy, atomic force microscopy, contact angle measurements, as well as near edge X-ray absorption fine structure (NEXAFS) microscopy and spectroscopy. The preparation methods explored should be extendable to a number of polymer systems.
Cancer gene therapy using a survivin mutant adenovirus (2001)

We have constructed a replication-deficient adenovirus encoding a nonphosphorylatable Thr34→Ala mutant of the apoptosis inhibitor survivin (pAd-T34A) to target tumor cell viability in vitro and in vivo. Infection with pAd-T34A caused spontaneous apoptosis in cell lines of breast, cervical, prostate, lung, and colorectal cancer. In contrast, pAd-T34A did not affect cell viability of proliferating normal human cells, including fibroblasts, endothelium, or smooth muscle cells. Infection of tumor cells with pAd-T34A resulted in cytochrome c release from mitochondria, cleavage of approximately 46-kDa upstream caspase-9, processing of caspase-3 to the active subunits of approximately 17 and 19 kDa, and increased caspase-3 catalytic activity. When compared with chemotherapeutic regimens, pAd-T34A was as effective as taxol and considerably more effective than adriamycin in induction of tumor cell apoptosis and enhanced taxol-induced cell death. In three xenograft breast cancer models in immunodeficient mice, pAd-T34A suppressed de novo tumor formation, inhibited by approximately 40% the growth of established tumors, and reduced intraperitoneal tumor dissemination. Tumors injected with pAd-T34A exhibited loss of proliferating cells and massive apoptosis by in situ internucleosomal DNA fragmentation. These data suggest that adenoviral targeting of the survivin pathway may provide a novel approach for selective cancer gene therapy.
Potential Neurotoxicity of Ketamine in the Developing Rat Brain (2009)

Ketamine, an N-methyl-D-aspartate (NMDA) receptor ion channel blocker, is a widely used anesthetic recently reported to enhance neuronal death in developing rodents and nonhuman primates. This study evaluated dose-response and time-course effects of ketamine, levels of ketamine in plasma and brain, and the relationship between altered NMDA receptor expression and ketamine-induced neuronal cell death during development. Postnatal day 7 rats were administered 5, 10, or 20 mg/kg ketamine using single or multiple injections (subcutaneously) at 2-h intervals, and the potential neurotoxic effects were examined 6 h after the last injection. No significant neurotoxic effects were detected in layers II or III of the frontal cortex of rats administered one, three, or six injections of 5 or 10 mg/kg ketamine. However, in rats administered six injections of 20 mg/kg ketamine, a significant increase in the number of caspase-3- and Fluoro-Jade C-positive neuronal cells was observed in the frontal cortex. Electron microscopic observations showed typical nuclear condensation and fragmentation indicating enhanced apoptotic characteristics. Increased cell death was also apparent in other brain regions. In addition, apoptosis occurred after plasma and brain levels of ketamine had returned to baseline levels. In situ hybridization also showed a remarkable increase in mRNA signals for the NMDA NR1 subunit in the frontal cortex. These data demonstrate that ketamine administration results in a dose-related and exposure-time dependent increase in neuronal cell death during development. Ketamine-induced cell death appears to be apoptotic in nature and closely associated with enhanced NMDA receptor subunit mRNA expression.
A Shared Task on Multimodal Machine Translation and Crosslingual Image Description (2016)

This paper introduces and summarises the findings of a new shared task at the intersection of Natural Language Processing and Computer Vision: the generation of image descriptions in a target language, given an image and/or one or more descriptions in a different (source) language. This challenge was organised along with the Conference on Machine Translation (WMT16), and called for system submissions for two task variants: (i) a translation task, in which a source language image description needs to be translated to a target language, (optionally) with additional cues from the corresponding image, and (ii) a description generation task, in which a target language description needs to be generated for an image, (optionally) with additional cues from source language descriptions of the same image. In this first edition of the shared task, 16 systems were submitted for the translation task and seven for the image description task, from a total of 10 teams.