gebhart/patrepeval huggingface dataset:
New developments in defecatory studies based on biomechatronics (2021)

Fecobionics measures well known parameters such as expulsion time and pressures as well as new metrics including defecation indices. The study suggests that Fecobionics is effective in evaluation of key defecatory parameters and well positioned as an integrated technology for assessment of anorectal function and dysfunction.
Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production (2009)

This result demonstrates that the elimination of genes unnecessary for cell growth can increase the productivity of an industrial strain, most likely by reducing the metabolic burden and improving the metabolic efficiency of cells.
Supplementary Figure 6 from Molecular Photoacoustic Imaging of Follicular Thyroid Carcinoma (2023)

&lt;p&gt;PDF file - 121K, Photoacoustic signal recorded at 680 and 750 nm&lt;/p&gt;
Comparing the bit-MAP and block-MAP decoding thresholds of reed-muller codes on BMS channels (2016)

The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory that was recently answered in the affirmative for transmission over erasure channels [1], [2]. Remarkably, the proof does not rely on specific properties of RM codes, apart from their symmetry. Indeed, the main technical result consists in showing that any sequence of linear codes, with doubly-transitive permutation groups, achieves capacity on the memoryless erasure channel under bit-MAP decoding. Thus, a natural question is what happens under block-MAP decoding. In [1], [2], by exploiting further symmetries of the code, the bit-MAP threshold was shown to be sharp enough so that the block erasure probability also converges to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel. We present an alternative approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds. This approach is based on a careful analysis of the weight distribution of RM codes. In particular, the flavor of the main result is the following: assume that the bit-MAP error probability decays as N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−δ</sup> , for some δ > 0. Then, the block-MAP error probability also converges to 0. This technique applies to transmission over any binary memoryless symmetric channel. Thus, it can be thought of as a first step in extending the proof that RM codes are capacity-achieving to the general case.
A New Action Potential Detector Using the MTEO and Its Effects on Spike Sorting Systems at Low Signal-to-Noise Ratios (2006)

This paper considers neural signal processing applied to extracellular recordings, in particular, unsupervised action potential detection at a low signal-to-noise ratio. It adopts the basic framework of the multiresolution Teager energy operator (MTEO) detector, but presents important new results including a significantly improved MTEO detector with some mathematical analyses, a new alignment technique with its effects on the whole spike sorting system, and a variety of experimental results. Specifically, the new MTEO detector employs smoothing windows normalized by noise power derived from mathematical analyses and has an improved complexity by utilizing the sampling rate. Experimental results prove that this detector achieves higher detection ratios at a fixed false alarm ratio than the TEO detector and the discrete wavelet transform detector. We also propose a method that improves the action potential alignment performance. Observing that the extreme points of the MTEO output are more robust to the background noise than those of the action potentials, we use the MTEO output for action potential alignment. This brings not only noticeable improvement in alignment performance but also quite favorable influence over the classification performance. Accordingly, the proposed detector improves the performance of the whole spike sorting system. We verified the improvement using various modeled neural signals and some real neural recordings.
Periodic Plasmonic/Dielectric Structures for SERS Applications (2009)

We propose a rational design towards amplifying the local electromagnetic (EM) field by integrating plasmonic optical antennas with periodic dielectric structures. The radiation process of an excited molecule placed on such devices is also studied.
Two‐dimensional multishot echo‐planar coronary MR angiography (1998)

This work presents a two-dimensional (2D) multishot echo-planar imaging (EPI) technique for magnetic resonance angiography (MRA) of individual coronary arteries in a 17-heartbeat breath-hold. Conventional 2D and 3D segmented gradient-echo (GRE) coronary MRA requires repetitive excitation of the same slice or slab within each cardiac cycle, which can result in reduced blood signal and in motion artifacts. Two-dimensional multishot EPI can address these limitations by eliminating multiple excitations per cardiac cycle, using large flip-angle excitations, markedly reducing the data acquisition window, and performing oblique multislice 2D imaging. The goal of this study was to assess the feasibility of breath-hold 2D multishot EPI for multislice coronary MRA and to demonstrate its reliability by consistently acquiring high-quality images of the coronary arteries in a series of 16 volunteers.
Directed Biosynthesis of Mitragynine Stereoisomers (2023)

<i>Mitragyna speciosa</i> ("kratom") is used as a natural remedy for pain and management of opioid dependence. The pharmacological properties of kratom have been linked to a complex mixture of monoterpene indole alkaloids, most notably mitragynine. Here, we report the central biosynthetic steps responsible for the scaffold formation of mitragynine and related corynanthe-type alkaloids. We illuminate the mechanistic basis by which the key stereogenic center of this scaffold is formed. These discoveries were leveraged for the enzymatic production of mitragynine, the C-20 epimer speciogynine, and fluorinated analogues.
Switches in Bacteriophage Lambda Development (2005)

The lysis-lysogeny decision of bacteriophage lambda (lambda) is a paradigm for developmental genetic networks. There are three key features, which characterize the network. First, after infection of the host bacterium, a decision between lytic or lysogenic development is made that is dependent upon environmental signals and the number of infecting phages per cell. Second, the lysogenic prophage state is very stable. Third, the prophage enters lytic development in response to DNA-damaging agents. The CI and Cro regulators define the lysogenic and lytic states, respectively, as a bistable genetic switch. Whereas CI maintains a stable lysogenic state, recent studies indicate that Cro sets the lytic course not by directly blocking CI expression but indirectly by lowering levels of CII which activates cI transcription. We discuss how a relatively simple phage like lambda employs a complex genetic network in decision-making processes, providing a challenge for theoretical modeling.
Immunoblastic lymphoma and thymic epithelial hyperplasia in angioimmunoblastic lymphadenopathy following gold therapy. (1985)

A 62-year-old woman with well-established polyarthritis developed angioimmunoblastic lymphadenopathy (AILD) during gold therapy. She subsequently developed an immunoblastic lymphoma which showed monoclonality (IgA, lambda) by immunoperoxidase techniques. There was a tumor-like enlargement of the thymus gland due to involvement by AILD, with secondary proliferation of thymic epithelium. The finding of thymic involvement, which has not been described previously in AILD, might be one of the manifestations reflecting a disturbance of the immune system in this disease.
Detection of biological signals from a live mammalian muscle using an early stage diamond quantum sensor (2021)

The ability to perform noninvasive and non-contact measurements of electric signals produced by action potentials is essential in biomedicine. A key method to do this is to remotely sense signals by the magnetic field they induce. Existing methods for magnetic field sensing of mammalian tissue, used in techniques such as magnetoencephalography of the brain, require cryogenically cooled superconducting detectors. These have many disadvantages in terms of high cost, flexibility and limited portability as well as poor spatial and temporal resolution. In this work we demonstrate an alternative technique for detecting magnetic fields generated by the current from action potentials in living tissue using nitrogen vacancy centres in diamond. With 50 pT/[Formula: see text] sensitivity, we show the first measurements of magnetic sensing from mammalian tissue with a diamond sensor using mouse muscle optogenetically activated with blue light. We show these proof of principle measurements can be performed in an ordinary, unshielded lab environment and that the signal can be easily recovered by digital signal processing techniques. Although as yet uncompetitive with probe electrophysiology in terms of sensitivity, we demonstrate the feasibility of sensing action potentials via magnetic field in mammals using a diamond quantum sensor, as a step towards microscopic imaging of electrical activity in a biological sample using nitrogen vacancy centres in diamond.
Knock‐down of the Cytoprotective Gene, Clusterin, to Enhance Hormone and Chemosensitivity in Prostate and Other Cancers (2005)

Discovery and targeting of genes mediating treatment resistance may lead to development of novel therapies that delay progression of recurrent and refractory cancers. Clusterin is a stress-associated cytoprotective chaperone expressed in many cancers that is upregulated in an adaptive cell survival manner by various apoptotic triggers and confers treatment resistance. Here, we review clusterin's functional role in regulating treatment-induced apoptosis and the use of a second generation antisense oligonucleotide to inhibit clusterin expression to enhance the cytotoxic effects of hormone- and chemotherapy in prostate and other xenograft models, as well as in recent human trials.
Sparse matrix-vector multiply on the HICAMP architecture (2012)

Sparse matrix-vector multiply (SpMV) is a critical task in the inner loop of modern iterative linear system solvers and exhibits very little data reuse. This low reuse means that its performance is bounded by main-memory bandwidth. Moreover, the random patterns of indirection make it difficult to achieve this bound. We present sparse matrix storage formats based on deduplicated memory. These formats reduce memory traffic during SpMV and thus show significantly improved performance bounds: 90x better in the best case. Additionally, we introduce a matrix format that inherently exploits any amount of matrix symmetry and is at the same time fully compatible with non-symmetric matrix code. Because of this, our method can concurrently operate on a symmetric matrix without complicated work partitioning schemes and without any thread synchronization or locking. This approach takes advantage of growing processor caches, but incurs an instruction count overhead. It is feasible to overcome this issue by using specialized hardware as shown by the recently proposed Hierarchical Immutable Content-Addressable Memory Processor, or HICAMP architecture.
Cav1.2 splice variant with exon 9* is critical for regulation of cerebral artery diameter (2009)

L-type voltage-dependent Ca(2+) channels (VDCCs) are essential for numerous processes in the cardiovascular and nervous systems. Alternative splicing modulates proteomic composition of Ca(v)1.2 to generate functional variation between channel isoforms. Here, we describe expression and function of Ca(v)1.2 channels containing alternatively spliced exon 9* in cerebral artery myocytes. RT-PCR showed expression of Ca(v)1.2 splice variants both containing (alpha(1)C(9/9*/10)) and lacking (alpha(1)C(9/10)) exon 9* in intact rabbit and human cerebral arteries. With the use of laser capture microdissection and RT-PCR, expression of mRNA for both alpha(1)C(9/9*/10) and alpha(1)C(9/10) was demonstrated in isolated cerebral artery myocytes. Quantitative real-time PCR revealed significantly greater alpha(1)C(9/9*/10) expression relative to alpha(1)C(9/10) in intact rabbit cerebral arteries compared with cardiac tissue and cerebral cortex. To demonstrate a functional role for alpha(1)C(9/9*/10), smooth muscle of intact cerebral arteries was treated with antisense oligonucleotides targeting alpha(1)C(9/9*/10) (alpha(1)C(9/9*/10)-AS) or exon 9 (alpha(1)C-AS), expressed in all Ca(v)1.2 splice variants, by reversible permeabilization and organ cultured for 1-4 days. Treatment with alpha(1)C(9/9*/10)-AS reduced maximal constriction induced by elevated extracellular K(+) ([K(+)](o)) by approximately 75% compared with alpha(1)C(9/9*/10-)sense-treated arteries. Maximal constriction in response to the Ca(2+) ionophore ionomycin and [K(+)](o) EC(50) values were not altered by antisense treatment. Decreases in maximal [K(+)](o)-induced constriction were similar between alpha(1)C(9/9*/10)-AS and alpha(1)C-AS groups (22.7 + or - 9% and 25.6 + or - 4% constriction, respectively). We conclude that although cerebral artery myocytes express both alpha(1)C(9/9*/10) and alpha(1)C(9/10) VDCC splice variants, alpha(1)C(9/9*/10) is functionally dominant in the control of cerebral artery diameter.
Expression of a GALACTINOL SYNTHASE Gene in Tomato Seeds Is Up-Regulated before Maturation Desiccation and Again after Imbibition whenever Radicle Protrusion Is Prevented (2003)

Raffinose family oligosaccharides (RFOs) have been implicated in mitigating the effects of environmental stresses on plants. In seeds, proposed roles for RFOs include protecting cellular integrity during desiccation and/or imbibition, extending longevity in the dehydrated state, and providing substrates for energy generation during germination. A gene encoding galactinol synthase (GOLS), the first committed enzyme in the biosynthesis of RFOs, was cloned from tomato (Lycopersicon esculentum Mill. cv Moneymaker) seeds, and its expression was characterized in tomato seeds and seedlings. GOLS (LeGOLS-1) mRNA accumulated in developing tomato seeds concomitant with maximum dry weight deposition and the acquisition of desiccation tolerance. LeGOLS-1 mRNA was present in mature, desiccated seeds but declined within 8 h of imbibition in wild-type seeds. However, LeGOLS-1 mRNA accumulated again in imbibed seeds prevented from completing germination by dormancy or water deficit. Gibberellin-deficient (gib-1) seeds maintained LeGOLS-1 mRNA amounts after imbibition unless supplied with gibberellin, whereas abscisic acid (ABA) did not prevent the loss of LeGOLS-1 mRNA from wild-type seeds. The presence of LeGOLS-1 mRNA in ABA-deficient (sitiens) tomato seeds indicated that wild-type amounts of ABA are not necessary for its accumulation during seed development. In all cases, LeGOLS-1 mRNA was most prevalent in the radicle tip. LeGOLS-1 mRNA accumulation was induced by dehydration but not by cold in germinating seeds, whereas both stresses induced LeGOLS-1 mRNA accumulation in seedling leaves. The physiological implications of LeGOLS-1 expression patterns in seeds and leaves are discussed in light of the hypothesized role of RFOs in plant stress tolerance.
Fabrication of Copper Matrix Composites and Simultaneous Bonding with Aluminum Alloy Using Combustion Reaction of Cu-Ti-B System (2004)

TiB2 particle reinforced Cu matrix composites were fabricated by a combustion reaction between Ti and B in a Cu-Ti-B system. Addition to the fabrication of the composite, its bonding with 1050 Al alloy were successfully carried out in a single-step process by using the high heat of the combustion reaction. When the combustion synthesis of Cu-50 vol%TiB2 was attempted, a minute quantity of unfavorable Cu3Ti was formed with TiB2 in the Cu matrix. However, for Cu-60 vol%TiB2, only fine TiB2 particles below 4 μm in diameter were formed in situ, and homogeneously distributed in the Cu matrix. Also for Cu-70 vol%TiB2, the combustion reaction occurred completely without forming any unfavorable phases, although some Cu was evaporated during synthesizing the composite. In a Ti-B binary system, any reaction was not generated in the temperature range from room temperature to 1473 K. However, in the Cu-Ti-B ternary system, the combustion reaction was generated near the melting point of Cu, suggesting that it was activated by molten Cu. Preheating before inducing the combustion reaction was effective in bonding with long Al rods and also in reducing bonding defects. Intermetallic compounds consisting of Al, Cu and Ti were observed with unreacted B in the bonded layer. For the bonded specimen with a Cu insert layer, a eutectic microstructure of Al and Cu was formed between the Al alloy and Cu insert, and unreacted B was observed with a compound of Cu and Ti between the composite and Cu insert. The bonding strength was improved by inserting the Cu layer and by preheating. The bonded specimen with no insert layer was fractured between the composite and the Al alloy. By inserting the Cu layer with preheating, the fracture occurred between the Al alloy and the Cu insert.
C/I gains in a single frequency network using TD-CDMA over a unicast network (2008)

This paper investigates the C/I gain of a Single Frequency Network for an MBSFN network using TDCDMA over an equivalent unicast network based on measurements from a trial network and simulations. It is shown that a cell edge C/I gain of 14.4 dB can be achieved in the trial network giving an increase of 59% in coverage by using a SFN over a unicast network.
Efficient ultraviolet Ce:LiSrAlF 6 laser using antisolarant pump beam (1996)

The introduction of a 532 nm Nd:YAG beam can be used to increase the slope efficiency of an ultraviolet Ce:LiSAF laser pumped at 266 nm by a factor of 1.4 by bleaching the color centers. The addition of a co-dopant, specifically sodium ions at a concentration of 2% in the melt also increases slope efficiency by a factor of 1.2.
Myocardial energetics (2022)

Abstract This chapter assesses myocardial energetics. The heart requires very large amounts of energy, cycling many times its own weight in ATP daily, and uses a variable combination of carbohydrates, lipids, lactate, and amino acids as fuel. A key feature of the healthy heart is ‘metabolic flexibility’, i.e. the ability to use different substrates according to circumstances. As the syndrome of heart failure progresses, a steady downregulation of all aspects of cardiac metabolism may be seen. In extreme disease states, a fundamental deficiency in ATP can be demonstrated, but more subtle metabolic abnormalities are detectable at an earlier stage. Additionally, there are multiple downstream disturbances in mitochondrial function, in the high-energy phosphate pool and in excitation–contraction coupling. Ultimately, the detection of abnormalities of myocardial metabolism and energetics has spurred an interest in therapeutic modulation of metabolism in heart failure. This is attractive, as potentially such modulation would improve myocardial efficiency without the need for increased fuel delivery. Such therapies could have an additive effect to current heart failure management which generally relies on correction of the maladaptive neurohumoral consequences of the heart failure syndrome.
Photoelectrochemical System: Conducting Polymers–Thylakoid Hybrid Materials for Water Oxidation and Photoelectric Conversion (Adv. Electron. Mater. 3/2019) (2019)

In article number 1800789, Fengting Lv, Hsiao-Hua Yu, Guillermo Bazan, Shu Wang, and co-workers report thylakoid photosynthesis enhancement by conductive polyelectrolytes. Poly(fluorene-co-phenylene) (PFP) accelerates the light-dependent reaction by Förster resonance energy transfer. Simultaneously, a well-matched redox potential promotes the electron transfer between thylakoids and electrode. Innovative hybrid biophotoelectrodes integrating conducting polymers into natural photosynthetic thylakoid therefore open new opportunities for solar energy utilization and renewable energy development.
The Importance of Cavitation Hysteresis in Megasonic Cleaning (2012)

An improved fundamental understanding of the megasonic cleaning process is necessary to optimize cleaning efficiency and minimize the unwanted damage to fragile structures. Argon sonoluminescence (SL) measurements are done to achieve an improved insight in the collapse threshold and behavior of microbubbles. This paper reports on acoustic cavitation by means of Ar Sonoluminescence (SL) investigation achieved with a dedicated test cell, a photomultiplier tube (PMT) and a gasification system. The results show an increase in SL signal as a function of the applied acoustic power density. An increase in Ar concentration results in a decrease in SL signal. Furthermore, a clear hysteretic behavior in the SL signal is identified when ramping the acoustic power up and down. This hysteresis effect can be attributed to the nucleation of bubbles during the increasing branch of the power loop. Finally the time evolution of SL light after the switching on of the acoustic transducers revealed the existence of a delay time.
POSTER (2017)

Manually labeling the large number of samples of Android APKs into benign or different malicious families requires tremendous human effort, while it is comparably easy and cheap to obtain a large amount of unlabeled APKs from various sources. Moreover, the fast-paced evolution of Android malware continuously generates derivative and new malware families. These families often contain new signatures, which can escape detection that uses static analysis. These practical challenges can also cause classical supervised machine learning algorithms to degrade in performance.
Estimation of Action/Reaction Forces for the Bilateral Control Using Kalman Filter (2011)

As haptic technology has advanced in the past decade, many sensor devices have been built and commercialized for providing the sense of action/reaction forces or moment feedback to the human operator. In the ideal bilateral control of the haptic system, the force and position control should achieve with the same actions of force and motion movements. An external force should be sensed quickly after contact with an unknown environment. This paper presents formulation and application of a Kalman filtering technique for control of master-slave robots contacting environment in a bilateral control. The different types of motion sensors are mounted on each robot to provide the position and acceleration data in the horizontal dimension. A Kalman-filter-based state observer and a Kalman-filter-based disturbance observer have been designed to estimate action/reaction forces. This paper also deals with the construction of bilateral control with the use of data provided by the different types of motion sensors. Compared to the other conventional disturbance observer or state observer, the bilateral control system based on the proposed method offers the advantages of wider bandwidth, faster response, and free from sensor noise. Thus, it is possible to provide high transparency and good perception of the environmental stiffness. The experimental results are provided to illustrate the performance of the proposed algorithms.