gebhart/patrepeval huggingface dataset:
Cepred: Predicting the Co-Expression Patterns of the Human Intronic microRNAs with Their Host Genes (2009)

Identifying the tissues in which a microRNA is expressed could enhance the understanding of the functions, the biological processes, and the diseases associated with that microRNA. However, the mechanisms of microRNA biogenesis and expression remain largely unclear and the identification of the tissues in which a microRNA is expressed is limited. Here, we present a machine learning based approach to predict whether an intronic microRNA show high co-expression with its host gene, by doing so, we could infer the tissues in which a microRNA is high expressed through the expression profile of its host gene. Our approach is able to achieve an accuracy of 79% in the leave-one-out cross validation and 95% on an independent testing dataset. We further estimated our method through comparing the predicted tissue specific microRNAs and the tissue specific microRNAs identified by biological experiments. This study presented a valuable tool to predict the co-expression patterns between human intronic microRNAs and their host genes, which would also help to understand the microRNA expression and regulation mechanisms. Finally, this framework can be easily extended to other species.
The Role of Toll-Like Receptors in Lung Transplantation (2012)

Lung transplantation is now a mainstream therapy for end-stage lung disease. However, long-term survival remains diminished by antigen-independent ischemia-reperfusion injury and antigendependent acute and chronic rejection. While rejection has traditionally been considered an adaptive immune response, the innate immune response, and events mediated by Toll-like receptors in particular, have recently been shown to be important to the priming and modulation of this adaptive immune response. Unlike other solid organ transplants, the lung is in constant communication with the outside environment and innate immunity likely plays a more significant role in lung transplantation. In this chapter, we will review Toll-like receptor responses in the context of lung transplantation.
SPADE: Sparsity-Adaptive Equalization for MMwave Massive MU-MIMO (2021)

We propose SParsity-ADaptive Equalization (SPADE), a novel approach to reduce the effective number of multiplications in sparse inner products by adaptively skipping multiplications that have little to no effect on the result. We apply SPADE to beamspace linear minimum mean square error (LMMSE) spatial equalization in all-digital millimeter-wave (mmWave) massive multiuser multiple-input multiple-output (MU-MIMO) systems. We propose a SPADE-based architecture that mutes insignificant multiplications to offer power savings. We use simulation results with line-of-sight (LoS) and non-LoS mmWave channel models to demonstrate that SPADE-LMMSE performs on par with state-of-the-art beamspace equalizers in terms of bit error-rate, while requiring significantly lower preprocessing complexity.
Thrombopoietin Is Synergistic with Other Cytokines for Expansion of Cord Blood Progenitor Cells (2000)

We investigated the effects of recombinant human thrombopoietin (TPO) in combination with various cytokines including erythropoietin (EPO), interleukin-3 (IL-3), interleukin-6 (IL-6), and stem cell factor (SCF) on megakaryopoiesis, and the expansion of CD34+CD41a+ cells from human cord blood CD34+ cells with these cytokines under serum-free conditions. Human cord blood CD34+ cells were cultured in Megacult (Stem Cell Technologies Inc. Vancouver, Canada) in the presence of recombinant growth factors. Colony-forming unit-megakaryocyte (CFU-M) colonies were counted on day 14. CD34+CD41a+ and CD34-CD41a+ cell expansion was analyzed using a serum-free liquid culture system for 7 days with recombinant growth factors. TPO alone had a concentration-dependent effect on megakaryocyte colony growth. At concentrations above 1 ng/ml, TPO supported significant CFU-Meg colony formation in a concentration-dependent manner. The combination of TPO plus other cytokines, including EPO, IL-3, and SCF, resulted in a synergistic enhancement of the number of CFU-Meg colonies, but IL-6 failed to enhance the effect of TPO. The number of CD41a+ cells increased after 7 days in liquid culture of human cord blood CD34+ cells with various cytokines (EPO, IL-3, IL-6, SCF) combined with TPO, but SCF plus TPO only resulted in a significant synergistic increment of CD34+CD41a+ cells compared with TPO alone. The results of the present study indicate that EPO, IL-3, and SCF can be synergistic with TPO to stimulate proliferation of CFU-Meg and suggest that SCF plus TPO can expand CD34+CD41a+ cells to effect the rapid recovery of platelets in patients following stem cell transplantation.
Activities of rumen micro-organisms in water buffalo (Bos bubalusL.) and in Zebu cattle (1969)

Summary Two fistulated adult bulls of the Zebu breed and 2 fistulated adult buffalo steers were given a diet consisting of concentrate mixture (rice bran and cotton-seed cake in equal portions +2% calcium hydroxide + 1% common salt) and straw. This was later changed to an all-roughage diet of first cut berseem ( Trifolium alexandrinum ) Samples of the rumen contents were taken for determination of protozoal differential counts, concentration and relative proportions of volatile fatty acids (VFA), rate of cellulose digestion, fermentation rate, and net growth of rumen micro-organisms. Further data were obtained for the 2 buffalo steers fed sweet Sudan grass. When the feed consisted of concentrate and straw there were significant differences in the numbers of protozoa and in volatile fatty acid concentration in the 2 species of animals. Higher protozoal counts were observed in the rumen of bulls (7·2−8·1 × 10 5 organisms/ml) than in the rumen of buffaloes (2·6−3·6 × 10 5 organisms/ml). Greater concentration of VFA was found in the rumen of buffaloes (5·3−11·2 mequiv/100 ml rumen liquor) than in bulls (4·8−10·4 m-equiv/100 ml rumen liquor). With berseem, the concentration of VFA in the rumen was generally higher (6·73−11·0 m-equiv/100 ml rumen liquor) and the protozoal counts were lower (2·8−5·2 × 10 5 organisms/ml) but there were no significant differences between bulls and buffaloes. The rates of cellulose digestion and the maximum fermentation rates were similar in the 2 species indicating a microbial population of the same order. Higher rates of cellulose digestion and of maximum fermentation when the ration consisted of berseem than when it consisted of concentrate + straw indicated a higher concentration of micro-organisms, mostly bacteria.
Induced Fit Interanion Discrimination by Binding-Induced Excimer Formation (2008)

The synthesis, photophysical, and anion-binding properties of a series of di-, tri-, and tetrapodal anion-binding hosts based on aminopyridinium units with pyrenyl reporter groups are described. The ditopic mesitylene-derived calix[4]arene-based host 4 binds strongly to dicarboxylates, particularly malonate, in a 2:1 anion:host ratio but is essentially nonemissive in the presence of all anions except chloride because of intramolecular quenching by the pyridinium units. Addition of chloride results in a conformational change, giving an initial increase in emission assigned to intramolecular excimer formation. Further chloride addition also results in an increase in the intensity of the pyrenyl monomer emission as chloride binding reduces the acceptor ability of the pyridinium groups. This behavior is not exhibited by control compounds 5 and 6, which lack the ditopic geometry and calixarene spacer unit; however, tripodal 6 forms 1:2 anion:host complexes with a range of anions.
Adsorption Properties of a Gold-Binding Peptide Assessed by its Attachment to a Recombinant Apoferritin Molecule (2008)

The adsorption properties of a recombinant apoferritin protein fused to a gold-binding peptide were characterized. The results of quartz crystal microbalance measurements showed that the fusion protein preferentially adsorbs to gold surfaces. Scanning electron microscopy also revealed that the protein selectively adsorbed onto a nanometer-scale gold pattern on a SiO2 surface fabricated by electron-beam lithography. Our results indicate that nanodots and nanowires synthesized using a biotemplate can be selectively placed onto a gold surface by genetically modifying the outer surface of the biotemplate. This technique represents an important step toward biotemplate-mediated fabrication of a nanometer-scaled device that utilizes gold electrodes.
Global Methylation Patterns in Idiopathic Pulmonary Fibrosis (2012)

Our results provide evidence that epigenetic changes in IPF are widespread and potentially important. The partial similarity to cancer may signify similar pathogenetic mechanisms while the differences constitute IPF or cancer specific changes. Elucidating the role of these specific changes will potentially allow better understanding of the pathogenesis of IPF.
2-Thiazolyl α-Amino Ketones: A New Class of Reactive Intermediates for the Stereocontrolled Synthesis of Unusual Amino Acids (1993)

The thiazole-based one carbon homologation of four α-amino acids (L-phenylalanine, L-leucine, L-threonine, and L-serine) to the corresponding α-hydroxy β-amino aldehydes and acids in both configurations at Cα, is described. The methodology involves the following key operations: (i) the conversion of an α-amino ester to a 2-thiazolyl α-amino ketone; (ii) the stereocontrolled reduction of a ketone carbonyl to either syn or anti α,β-amino alcohols; (iii) the aldehyde release from the thiazole ring; (iv) the oxidation of the aldehyde to a carboxylic acid. The methodology was only partially applied to L-phenylglycine because of some limitations in operation (i).
<title>Electronically Scanned Phased Arrays For Near Millimeter Wave Imaging In A Dynamic Tactical Environment</title> (1981)

The Electronically Scanned Phased Array concept is considered as a technique for obtaining near millimeter (NIVIM) wave imaging. Consideration is given to the various factors of importance for obtaining near millimeter images in a dynamic tactical environment.
Determination of the activation parameters and the mechanism for atropisomerization of (S )-3-(2-chlorophenyl)-2-[2-(6-diethylaminomethylpyridin-2-yl)vinyl]-6-fluoroquinazolin-4(3H )-one † (2001)

Values of ΔH‡ = 111.6 ± 0.3 kJ mol−1 (26.7 ± 0.1 kcal mol−1) and ΔS‡ = −25.7 ± 0.9 J K−1 mol−1 (−6.1 ± 0.2 cal K−1 mol−1) have been determined for the atropisomerization of (S)-3-(2-chlorophenyl)-2-[2-(6-diethylaminomethylpyridin-2-yl)vinyl]-6-fluoroquinazolin-4(3H)-one in decane. Based on molecular mechanics calculations in the literature and an observation that more polar solvent does not increase isomerization rate, it is proposed that the isomerization occurs via a planar non-ionic transition state in which the carbonyl oxygen and the 6-chloro substituent are coplanar with each other.
Personal Computers in Laboratory Teaching of Control (1993)

SUMMARY This paper reports on the incorporation of personal computers in the laboratory program at UMIST's Control Systems Centre. Laboratory practice is an integral component of all our control course. The laboratory facilities provide a mechanism for testing and verifying theoretical and design approaches. Incorporating computers in all phases of the laboratory program makes possible the use of current techniques in the analysis and design of realistic control systems. The control systems laboratory at UMIST has been developed with the goal of providing real world analysis and design experience in a laboratory setting. A collection of scale model experiments representing the major categories of industrial control problems has been constructed. These working models are coupled with a standard instrumentation interface and analogue and digital computers to implement control strategies. In all cases, great care has been taken to retain realism and allow the student to concentrate on control issues rather than configuration or programming problems. The primary objective of using personal computers in the control laboratory is to provide an on-line link between the student and the laboratory model. This provides direct ‘hands on’ experience of digital control ideas, interactive digital control experimentation and use of the computer as a multi-function virtual instrument. In addition, the computer is used off-line to simulate model performance as various control strategies are tried. At this point in time, each laboratory model station has been equipped with a personal computer containing A/D and D/A converters, hard and floppy disk, and a real-time clock. The computers are networked to provide access to printing and file storage facilities. Originally the software packages were written primarily in BASIC, and ran on BBC computers. These versions are however in the process of being replaced by PC-based packages written in C. Both the original BASIC and the C-successors have been developed to provide interactive, real-time control of the model using a choice of digital control algorithms. Using the keyboard as a control panel, the student can observe model performance, vary controller parameters, choose display characteristics and record parametric and graphical data. Future developments will expand the choice of available control algorithms and enhance the off-line analysis and design tools.
Parkinson's disease, dementia with Lewy bodies, multiple system atrophy and the spectrum of diseases with α-synuclein inclusions (2004)

Synucleinopathies are a group of neurodegenerative disorders sharing in common the presence of intracellular fibrillar inclusions composed of polymerized α-synuclein (α-syn). Although the biological function of this presynaptic protein remains largely unknown, overwhelming evidence indicates that its self-aggregation in neurons and/or oligodendrocytes is associated with the impairment of nervous system function and cellular demise leading to disease. Pathological inclusions composed of α-syn have been the focus of enumerable clinical and pathological studies with the earliest dating almost to the beginning of the twentieth century. However, the finding that these inclusions are comprised of α-syn only became apparent in the past 5 years following the identification of a mutation in the α-syn gene in families with Parkinson's disease. α-Syn inclusions are the defining characteristics of several disorders including Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). However, they are also found in a significant percentage of other neurodegenerative disorders including neurodegeneration with brain iron accumulation type-1 (NBIA-1), Down's syndrome, and familial and sporadic Alzheimer's disease (AD) (Table 15.1). The understanding of the role of α-syn in neurodegenerative disease requires the determination of the normal function and properties of this protein, the clinicopathological assessment of the relationship between α-syn inclusions and disease, and the elucidation of the mechanism of pathogenesis. In this chapter, we will focus on the most recent developments in these aspects of synucleinopathies, but the description of these diseases also requires an overview of the most significant features that have been documented for over almost 100 years.
Metastatic seeding of human colon cancer cell clusters expressing the hybrid epithelial/mesenchymal state (2019)

Emerging evidence supports the theory that tumor cell clusters efficiently metastasize to distant organs. However, the roles of epithelial-to-mesenchymal transition (EMT) in metastasizing tumor cell clusters have not yet been fully elucidated. To investigate this issue, tumor fragments were dissected from 40 colorectal cancer (CRC) patients and implanted subcutaneously into immunodeficient mice. We observed that tumors developed from the tumor fragments obtained from 28 of the 40 CRC patients. The tumors were then dissociated into cell suspensions to be orthotopically injected into secondary mice. The tumors from 13 of the 28 patients progressed. Furthermore, metastases formed spontaneously in the liver and lungs from the tumor fragments obtained from 8 of these 13 patients. Moreover, employing a mathematical analysis, we showed that tumor cell clusters seeded these metastases significantly more often than did single tumor cells. Membrane E-cadherin- and nuclear ZEB1-positive tumor cells indicating the hybrid epithelial/mesenchymal state were also detected in primary tumors of various CRC patients, and in the corresponding patient-derived xenografts (PDXs) and circulating tumor cell clusters in the bloodstreams of mice. In contrast, ZEB1 staining was barely detectable in the patient-matched liver metastases presumably developing through mesenchymal-to-epithelial transition. Inhibition of E-cadherin or ZEB1 expression by shRNA notably prevented the PDX-derived tumor organoids from colonizing the liver, when injected intrasplenically into mice, indicating E-cadherin and ZEB1 expressions to be required for their metastatic colonization. Taken together, these findings suggest that the epithelial/mesenchymal state mediates metastatic seeding of human CRC cell clusters into distant organs.
How ordinary internet users can have a chance to influence privacy policies (2006)

By 'Obligation Management' we refer to the definition, automated enforcement, and monitoring of privacy obligation policies. Privacy policies are nowadays found on most organisations' web pages, especially when data is directly collected from the user/customer. The paper demonstrates how users can influence rather than merely accept a privacy policy, and further relates this to the larger framework within which policy compliance should be discussed. Four problem areas are identified (from design studies and user tests with paper and computer-based mock-ups): trustworthiness, enterprise perspective, phrases, and obligation setting relative to data or data collection purpose.
Observations from Chaotic Analysis of Sleep EEGs (2006)

Chaotic analysis and modeling methods were applied to a small collection of healthy individuals' sleeping EEGs in order to establish whether a common representational space could be discovered for use in comparative analysis. Common challenges were encountered and dealt with in a practical manner. The methods used and the choices made in this effort are described herein. The authors observe and describe a common representation, obtained from a delay coordinate embedding, that should be usable for comparative analysis leading to clinical utility.
An integrated approach to recovery and high availability in an updatable, distributed data warehouse (2006)

Any highly available data warehouse will use some form of data replication to tolerate machine failures. In this paper, we demonstrate that we can leverage this data redundancy to build an integrated approach to recovery and high availability. Our approach, called HARBOR, revives a crashed site by querying remote, online sites for missing updates and uses timestamps to determine which tuples need to be copied or updated. HARBOR does not require a stable log, recovers without quiescing the system, allows replicated data to be stored non-identically, and is simpler than a log-based recovery algorithm.We compare the runtime overhead and recovery performance of HARBOR to those of two-phase commit and ARIES, the gold standard for log-based recovery, on a three-node distributed database system. Our experiments demonstrate that HARBOR suffers lower runtime overhead, has recovery performance comparable to ARIES's, and can tolerate the fault of a worker and efficiently bring it back online.
Interconnections in Multi-Core Architectures: Understanding Mechanisms, Overheads and Scaling (2005)

This paper examines the area, power, performance, and design issues for the on-chip interconnects on a chip multiprocessor, attempting to present a comprehensive view of a class of interconnect architectures. It shows that the design choices for the interconnect have significant effect on the rest of the chip, potentially consuming a significant fraction of the real estate and power budget. This research shows that designs that treat interconnect as an entity that can be independently architected and optimized would not arrive at the best multi-core design. Several examples are presented showing the need for careful co-design. For instance, increasing interconnect bandwidth requires area that then constrains the number of cores or cache sizes, and does not necessarily increase performance. Also, shared level-2 caches become significantly less attractive when the overhead of the resulting crossbar is accounted for. A hierarchical bus structure is examined which negates some of the performance costs of the assumed base-line architecture.
Oxidative Stress Activates the Human Histidine Decarboxylase Promoter in AGS Gastric Cancer Cells (1998)

Oxidant stress is thought to play a role in the pathogenesis of many gastric disorders. We have recently reported that histidine decarboxylase (HDC) promoter activity is stimulated by gastrin through a protein kinase C- and extracellular signal-regulating kinase (ERK)-dependent pathway in gastric cancer (AGS-B) cells, and this transcriptional response is mediated by a downstream cis-acting element, the gastrin response element (GAS-RE). To study the mechanism through which oxidant stress affects gastric cells, we examined the effects of hydrogen peroxide (H2O2) on HDC promoter activity and intracellular signaling in AGS-B cells. H2O2 (10 mM) specifically activated the HDC promoter 10-12-fold, and this activation was blocked by both mannitol and N-acetylcysteine. Hydrogen peroxide treatment of AGS-B cells increased the phosphorylation and kinase activity of ERK-1 and ERK-2, but did not affect Jun kinase tyrosine phosphorylation or kinase activity. In addition, treatment of AGS-B cells with H2O2 resulted in increased c-fos/c-jun mRNA expression and AP-1 activity, and also led to increased phosphorylation of epidermal growth factor receptor (EGFR) and Shc. H2O2-dependent stimulation of HDC promoter activity was completely inhibited by kinase-deficient ERKs, dominant-negative (N17 and N15) Ras, and dominant-negative Raf, and partially blocked by a dominant-negative EGFR mutant. In contrast, protein kinase C blockade did not inhibit H2O2-dependent induction of the HDC promoter. Finally, deletion analysis demonstrated that the H2O2 response element could be mapped to the GAS-RE (nucleotides 2 to 24) of the basal HDC promoter. Overall, these studies suggest that oxidant stress activates the HDC promoter through the GAS-RE, and through an Ras-, Raf-, and ERK-dependent pathway at least partially involving the EGFR.
Management of Disseminated Midgut Carcinoid Tumours (1991)

Forty-one patients with disseminated midgut carcinoid tumours were treated over a 6-year period according to a strict programme including primary surgical treatment. In 10 patients, a total remission of the disease was obtained. Patients with bilobar hepatic disease had ischaemic treatment of their liver metastases by hepatic arterial embolisation after primary surgical and medical treatment (low dose octreotide). Thus, by combining surgical, radiological and medical treatment modalities, we wanted to offer these patients optimal palliation. This treatment programme resulted in good symptomatic relief in all patients accompanied by a marked reduction in 5-hydroxyindoleacetic acid (5-HIAA) levels. At recurrence of symptoms in combination with rising 5-HIAA levels, embolisation was repeated. Ten of the treated patients have deceased during the observation period, but only 5 from their carcinoid disease.