gebhart/patrepeval huggingface dataset:
Pairwise-Constrained Implicit Functions for 3D Human Heart Modelling (2023)

Accurate 3D models of the human heart require not only correct outer surfaces but also realistic inner structures, such as the ventricles, atria, and myocardial layers. Approaches relying on implicit surfaces, such as signed distance functions (SDFs), are primarily designed for single watertight surfaces, making them ill-suited for multi-layered anatomical structures. They often produce gaps or overlaps in shared boundaries. Unsigned distance functions (UDFs) can model non-watertight geometries but are harder to optimize, while voxel-based methods are limited in resolution and struggle to produce smooth, anatomically realistic surfaces. We introduce a pairwise-constrained SDF approach that models the heart as a set of interdependent SDFs, each representing a distinct anatomical component. By enforcing proper contact between adjacent SDFs, we ensure that they form anatomically correct shared walls, preserving the internal structure of the heart and preventing overlaps, or unwanted gaps. Our method significantly improves inner structure accuracy over single-SDF, UDF-based, voxel-based, and segmentation-based reconstructions. We further demonstrate its generalizability by applying it to a vertebrae dataset, preventing unwanted contact between structures.
Optical microphone based on a modulated diffractive lens (2003)

The authors present an optical microphone based on a diffractive lens. The distance between the diffractive lens and a reflecting microphone membrane determines the light intensity at the focal point of the lens. With this design, an integrated micromachined microphone transducer can be mass produced at low cost. They describe the sensing principle, calculate the intensity at the focal point, and show how it depends on the membrane position. The authors present results from measurements with a prototype setup which proves the measurement principle and has excellent properties when compared to an expensive condenser microphone.
T-BASIR: Finding Shutdown Bugs for Cloud-Based Applications in Cloud Spot Markets (2020)

One of the major advantages of cloud spot instances in cloud computing is to allow stakeholders to economically deploy their applications at much lower costs than that of other types of cloud instances. In exchange, spot instances are often exposed to revocations (i.e., terminations) by cloud providers. With spot instances becoming pervasive, terminations have become a part of the normal behavior of cloud-based applications; thus, these applications may be left in an incorrect state leading to certain bugs. Unfortunately, these applications are not designed or tested to deal with this behavior in the cloud environment, and as a result, the advantages of cloud spot instances could be significantly minimized or even entirely negated. We propose a novel solution to automatically find these bugs and locate their causes in the source code. We evaluate our solution using 10 popular open-source applications. The results show that our solution not only finds more instances and different types of these bugs compared to the random approach, but it also locates the causes of these bugs to help developers improve the design of the shutdown process and is more efficient in finding instances of these bugs since it interposes at the system call layer.
Non-linear Fourier Time Series Analysis for Human Brain Mapping by Functional Magnetic Resonance Imaging (1997)

SUMMARY A non-linear parametric model for brain activation detection by functional magnetic resonance imaging (FMRI) is proposed. The effects of a designed temporal stimulus on the FMRI signal at each brain location in a 36×60 spatial grid are estimated from discrete Fourier transforms of the observed time series at each location. The frequency domain regression model accommodates unobservable and spatially varying haemodynamic response functions through their estimated convolutions with the global stimulus. This approach generalizes an existing method for human brain mapping. An experiment to detect focal cortical activation during primary visual stimulation demonstrates the usefulness of the method.
Anisotropic smoothing regularization (AnSR) in Thirion's Demons registration evaluates brain MRI tissue changes post-laser ablation (2013)

MRI-guided laser-induced interstitial thermal therapy (LITT) is a form of laser ablation and a potential alternative to craniotomy in treating glioblastoma multiforme (GBM) and epilepsy patients, but its effectiveness has yet to be fully evaluated. One way of assessing short-term treatment of LITT is by evaluating changes in post-treatment MRI as a measure of response. Alignment of pre- and post-LITT MRI in GBM and epilepsy patients via nonrigid registration is necessary to detect subtle localized treatment changes on imaging, which can then be correlated with patient outcome. A popular deformable registration scheme in the context of brain imaging is Thirion's Demons algorithm, but its flexibility often introduces artifacts without physical significance, which has conventionally been corrected by Gaussian smoothing of the deformation field. In order to prevent such artifacts, we instead present the Anisotropic smoothing regularizer (AnSR) which utilizes edge-detection and denoising within the Demons framework to regularize the deformation field at each iteration of the registration more aggressively in regions of homogeneously oriented displacements while simultaneously regularizing less aggressively in areas containing heterogeneous local deformation and tissue interfaces. In contrast, the conventional Gaussian smoothing regularizer (GaSR) uniformly averages over the entire deformation field, without carefully accounting for transitions across tissue boundaries and local displacements in the deformation field. In this work we employ AnSR within the Demons algorithm and perform pairwise registration on 2D synthetic brain MRI with and without noise after inducing a deformation that models shrinkage of the target region expected from LITT. We also applied Demons with AnSR for registering clinical T1-weighted MRI for one epilepsy and one GBM patient pre- and post-LITT. Our results demonstrate that by maintaining select displacements in the deformation field, AnSR outperforms both GaSR and no regularizer (NoR) in terms of normalized sum of squared differences (NSSD) with values such as 0.743, 0.807, and 1.000, respectively, for GBM.
The chemokine Bv8/prokineticin 2 is up-regulated in inflammatory granulocytes and modulates inflammatory pain (2009)

Neutrophil migration into injured tissues is invariably accompanied by pain. Bv8/prokineticin 2 (PK2), a chemokine characterized by a unique structural motif comprising five disulfide bonds, is highly expressed in inflamed tissues associated to infiltrating cells. Here, we demonstrate the fundamental role of granulocyte-derived PK2 (GrPK2) in initiating inflammatory pain and driving peripheral sensitization. In animal models of complete Freund's adjuvant-induced paw inflammation the development and duration of pain temporally correlated with the expression levels of PK2 in the inflamed sites. Such an increase in PK2 mRNA depends mainly on a marked up-regulation of PK2 gene transcription in granulocytes. A substantially lower up-regulation was also detected in macrophages. From a pool of peritoneal granulocytes, elicited in rats by oyster glycogen, we purified the GrPK2 protein, which displayed high affinity for the prokineticin receptors (PKRs) and, when injected into the rat paw, induced hypersensitivity to noxious stimuli as the amphibian prokineticin Bv8 did. Mice lacking PKR1 or PKR2 developed significantly less inflammation-induced hyperalgesia in comparison with WT mice, confirming the involvement of both PKRs in inflammatory pain. The inflammation-induced up-regulation of PK2 was significantly less in pkr1 null mice than in WT and pkr2 null mice, demonstrating a role of PKR1 in setting PK2 levels during inflammation. Pretreatment with a nonpeptide PKR antagonist, which preferentially binds PKR1, dose-dependently reduced and eventually abolished both prokineticin-induced hypernociception and inflammatory hyperalgesia. Inhibiting PK2 formation or antagonizing PKRs may represent another therapeutic approach for controlling inflammatory pain.
Peripheral Processes in Insect Olfaction (1992)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
<title>On-groove phase-change optical recording for a capacity of 25 GB</title> (2002)

The possibility of high-density groove-only recording was investigated by using a high-numerical-aperture lens unit and an InGaN semiconductor laser. Wobbled grooves of 20 nm in depth were formed through a deep-UV disk mastering process and replicated by injection molding onto a polycarbonate disk substrate. This shallow wobbled groove structure improves a signal-to-noise ratio (SNR) and also enables an address in pre-grooves (ADIP). In the experiment, signals were recorded either in or on the grooves, and the achievable areal recording density was carefully examined in each case, comparing with a previous land-and-groove disk configuration. The authors' results indicate that the signal recording on the grooves, which correspond to the structured area located closer to the objective lens, brings higher track density than that in the grooves. A bit size of 120 X 320 nm, an areal density of 16.8 Gbit/in<SUP>2</SUP>, was verified at the data transfer rate of 35 Mbps on a phase-change disk of SbTe-based eutectic composition. This bit density can realize a storage capacity of 23.3 GB on a f 120 mm disk. Further investigation on higher areal density was also examined with an additional signal processing.
Neurofilaments Are Nonessential to the Pathogenesis of Toxicant-Induced Axonal Degeneration (2001)

Axonal neurofilament (NF) accumulations occur before development of symptoms and before other pathological changes among idiopathic neurodegenerative diseases and toxic neuropathies, suggesting a cause-effect relationship. The dependence of symptoms and axonal degeneration on neurofilament accumulation has been tested here in a transgenic mouse model (Eyer and Peterson, 1994) lacking axonal NFs and using two prototypic toxicant models. Chronic acrylamide (ACR) or 2,5-hexanedione exposure resulted in progressive and cumulative increases in sensorimotor deficits. Neurobehavioral tests demonstrated similar expression of neurotoxicity in transgenic (T) mice and their nontransgenic (NT) littermates (containing normal numbers of axonal NFs). Axonal lesions were frequently observed after exposure to either toxicant. Quantitation of ACR-induced lesions demonstrated the distal location of pathology and equal susceptibility of T and NT axons. We conclude that axonal NFs have no effect on neurotoxicity and the pattern of pathology in these mammalian toxic neuropathies. These results also suggest that the role of neurofilament accumulation in the pathogenesis of neurodegenerative diseases requires careful evaluation.
Enhanced synthesis of hyaluronic acid by human gingival fibroblasts exposed to human dental bacterial extract (1983)

Hyaluronic acid synthesis was studied in human gingival fibroblast cultures exposed to human dental bacterial plaque extract. The cells were stimulated to produce large amounts of hyaluronic acid (HA) into the culture medium. The extract did not have any direct effect on the activity of hyaluronic acid synthetase enzyme complex, indicating that the increased hyaluronic acid synthesis was caused by metabolic alterations in gingival cells. Dental plaque extract also decreased the molecular weight of hyaluronic acid. This was obviously caused by the plaque derived hyaluronidase, because denaturation of plaque proteins by heating prevented this degradation. On the other hand, the stimulatory effect on the HA synthesis by the plaque extract was not destroyed by heating. The increased production of low molecular weight HA by gingival fibroblasts after plaque exposure is suggested to have a role in the pathogenesis of chronic periodontal disease in vivo .
Poly(A) Binding Protein C1 Is Essential for Efficient L1 Retrotransposition and Affects L1 RNP Formation (2012)

Poly(A) binding proteins (PABPs) specifically bind the polyadenosine tail of mRNA and have been shown to be important for RNA polyadenylation, translation initiation, and mRNA stability. Using a modified L1 retrotransposition vector, we examined the effects of two PABPs (encoded by PABPN1 and PABPC1) on the retrotransposition activity of the L1 non-long-terminal-repeat (non-LTR) retrotransposon in both HeLa and HEK293T cells. We demonstrated that knockdown of these two genes by RNA interference (RNAi) effectively reduced L1 retrotransposition by 70 to 80% without significantly changing L1 transcription or translation or the status of the poly(A) tail. We identified that both poly(A) binding proteins were associated with the L1 ribonucleoprotein complex, presumably through L1 mRNA. Depletion of PABPC1 caused a defect in L1 RNP formation. Knockdown of the PABPC1 inhibitor PAIP2 increased L1 retrotransposition up to 2-fold. Low levels of exogenous overexpression of PABPN1 and PABPC1 increased L1 retrotransposition, whereas unregulated overexpression of these two proteins caused pleiotropic effects, such as hypersensitivity to puromycin and decreased L1 activity. Our data suggest that PABPC1 is essential for the formation of L1 RNA-protein complexes and may play a role in L1 RNP translocation in the host cell.
Cyclobutanones via the (1‐Oxycyclopropyl)methanol Route (1977)

Abstract A variety of alcohols of the 1‐oxycyclopropyl structure, prapared mostly from α‐alkoxy‐α,β‐unsaturated ketnnes and esters by way of reductinn and Simmons ‐ Smith reaction of the resultant α‐alkoxyallyl alcohols, are shown to rearrange into cyclobutanones on acid treatment ( cf. Scheme 1 ).
Examination of antenna combinations for UWB ranging system (2006)

In this paper, several combinations of antennas for ultra-wideband (UWB) ranging are examined. Due to the large bandwidth of the pulse signal, wideband antennas are generally required. Depending on the characteristics of the antennas, the pulse waveform is distorted and the received signal power is reduced. This may increase the timing errors of synchronization at the receiver. Therefore, the characteristics of transmission and reception antennas influence the accuracy of ranging capability. In this paper, the received pulse waveform with different combinations of transmission and reception antennas is measured, and the performance of the pulse synchronization scheme applied for UWB ranging is investigated. It is shown through computer simulation that the received signal with the wideband antennas suffers from the least path loss. However, for the purpose of ranging with a high-speed comparator, the degradation on the estimation performance due to the use of the monopole antenna is limited and it can be used in the transmitter of RF tag systems.
Prostate Organoid Cultures as Tools to Translate Genotypes and Mutational Profiles to Pharmacological Responses (2019)

Presented here is a protocol to study pharmacodynamics, stem cell potential, and cancer differentiation in prostate epithelial organoids. Prostate organoids are androgen responsive, three-dimensional (3D) cultures grown in a defined medium that resembles the prostatic epithelium. Prostate organoids can be established from wild-type and genetically engineered mouse models, benign human tissue, and advanced prostate cancer. Importantly, patient derived organoids closely resemble tumors in genetics and in vivo tumor biology. Moreover, organoids can be genetically manipulated using CRISPR/Cas9 and shRNA systems. These controlled genetics make the organoid culture attractive as a platform for rapidly testing the effects of genotypes and mutational profiles on pharmacological responses. However, experimental protocols must be specifically adapted to the 3D nature of organoid cultures to obtain reproducible results. Described here are detailed protocols for performing seeding assays to determine organoid formation capacity. Subsequently, this report shows how to perform drug treatments and analyze pharmacological response via viability measurements, protein isolation, and RNA isolation. Finally, the protocol describes how to prepare organoids for xenografting and subsequent in vivo growth assays using subcutaneous grafting. These protocols yield highly reproducible data and are widely applicable to 3D culture systems.
Self‐organized Ruthenium–Barium Core–Shell Nanoparticles on a Mesoporous Calcium Amide Matrix for Efficient Low‐Temperature Ammonia Synthesis (2018)

A low-temperature ammonia synthesis process is required for on-site synthesis. Barium-doped calcium amide (Ba-Ca(NH<sub>2</sub> )<sub>2</sub> ) enhances the efficacy of ammonia synthesis mediated by Ru and Co by 2 orders of magnitude more than that of a conventional Ru catalyst at temperatures below 300 °C. Furthermore, the presented catalysts are superior to the wüstite-based Fe catalyst, which is known as a highly active industrial catalyst at low temperatures and pressures. Nanosized Ru-Ba core-shell structures are self-organized on the Ba-Ca(NH<sub>2</sub> )<sub>2</sub> support during H<sub>2</sub> pretreatment, and the support material is simultaneously converted into a mesoporous structure with a high surface area (>100 m<sup>2</sup> g<sup>-1</sup> ). These self-organized nanostructures account for the high catalytic performance in low-temperature ammonia synthesis.
1126: A New Classification of Phenotype-Genotype of Cystinuria Patients in Japan (2004)

rBAT) result in cystinuria. We have analyzed 41 cystinuria patients from oriental (Japanese and Korean) population and found that the mutations of SLC7A9 are quite different from those previously reported. 90% of patients who have mutations in SLC7 A9 possess one single mutation which has never been found in European and American population. We have analyzed this mutation in order to understand the mechanisms of oriental type of cystinuria and provide a new insight into the mechanisms of disease.
Low-voltage, N-channel transistors including a hybrid semiconductor-dielectric material (2023)

Hybrid semiconducting-dielectric materials and electronic or electro-optic devices using the hybrid semiconducting-dielectric materials. Hybrid semiconducting-dielectric materials comprise molecules that have a core section that provides an n-type semiconducting property and side chains that provide a dielectric property to a layer of hybrid semiconducting-dielectric material. Specific hybrid semiconducting-dielectric materials include tetracarboxylic diimide compounds having sidechains comprising fluorine substituted aliphatic or aromatic moieties linked to the tetracarboxylic diimide structure by an alkylene or heteroalkylene linking group.
Joint Spatio-temporal Neural Source Reconstruction Using Electroencephalography and Near-infrared Spectroscopy (2020)

Electroencephalography (EEG) and near-infrared spectroscopy (NIRS) are commonly used for neural source reconstruction, but have limited spatial or temporal resolution. Using NIRS reconstruction as a spatial prior for EEG reconstruction, neural sources are spatio-temporally reconstructed.
“Tyranny of writing” and English corpus linguistics : What to do with the new mediated and vernacular genres? (2014)

This presentation discusses ongoing research that focuses on exploring grammatical variability in advanced L2 uses of English in the expanding circle, i.e. in countries in which English does not have an official role but where it is widely used as a linguistic resource in today’s globalized world. This research is corpus-based, and my presentation focuses on the sources of evidence using the notion of “tyranny of writing”. For instance, up to today, most of the existing corpus materials from the expanding circle consist of learner corpora which are collections of short written essays collected from institutional settings. They are excellent tools but exclude a wide range of new mediated and vernacular genres. Similarly, the corpora from the inner core varieties of English, i.e. American and British English, contain materials from a variety of formal written genres, covering texts types of news, academic and fiction, etc. This presentation discusses how to make use of these best practices in English corpus linguistics to create a set of corpora of English use in the expanding circle. These new corpora should ideally represent not only formal written genres but also a wide range of vernacular genres, such as blogs, news-letters, Twitter messages, where English is used, but at the same time, these new sources of evidence should be comparable with the existing corpora in order to ensure diachronic comparisons.
Active/Passive Switching Control Framework for Assistive Devices with Variable Stiffness Actuator (2019)

Actuators for physical human-robot interaction, such as series elastic actuators, have been investigated for use in assistive systems. The authors have explored a pneumatic actuator working as a passive spring with controllable stiffness and equilibrium point. This actuator has the potential to allow assistive devices to balance the competing goals of maximizing user assistance while minimizing the energy consumption of the devices. This paper introduces a novel switching control framework for assistive devices that use the pneumatic actuator to achieve these goals. A simulation study is conducted to confirm the performance of the proposed framework. The results suggest the proposed framework can find the required assistance without extraneous air consumption, which reduces the user's joint torque by 13% compared with the torque in the no-assist case. Further, the assistive device can reduce the user's joint torque by half at the expense of some air consumption. From these observations, we conclude that the proposed framework could be utilized to balance the amount of assistance and energy consumption according to the user's situation.
Bootstrap Bayesian analysis with applications to gene-environment interaction (2009)

We propose a novel statistical model and inferential algorithm for gene environment interaction. Our methodology was motivated by and applied to identity by descent (IBD) sharing for sibling pairs affected by schizophrenia. Our analysis confirms some of the previous findings on the same data set, e.g. the estimated location of the disease gene and the existence of the interaction between the location of disease gene and environment. Our analysis also provides new insights by better accounting for overall variability in the data. We show that taking into account sampling variability may increase the length of posterior credible intervals for the true location of the disease gene by as much as 140%. Moreover, the posterior distribution is shown to be non-Gaussian, which more closely matches the data.
Advances in hardware design and implementation of signal processing systems [DSP Forum] (2008)

This IEEE Signal Processing Magazine (SPM) forum discusses advances, challenges, and future trends in hardware design and implementation of signal processing (SP) systems. The invited forum members who bring their expert insights are: Prof. Shuvra S. Bhattacharyya (University of Maryland, College Park), Jeff Bier [Berkeley Design Technology, Inc. (BDTI)], Dr. Wanda K. Gass (Texas Instruments), Dr. Ram K. Krishnamurthy (Intel), and Prof. Edward A. Lee (Univerisity of California, Berkeley and BDTI). The moderator of the forum is Dr. Konstantinos Konstantinides (Hewlett-Packard and associate editor of SPM). Our readers may agree or disagree with the ideas discussed next. In either case, we invite you to share your comments with us by e-mailing to SPM_columns_forums@yahoo.com