gebhart/patrepeval huggingface dataset:
Obstructions to classically simulating the quantum adiabatic algorithm (2013)

We consider the adiabatic quantum algorithm for systems with ``no sign problem", such as the transverse field Ising model, and analyze the equilibration time for quantum Monte Carlo (QMC) on these systems. We ask: if the spectral gap is only inverse polynomially small, will equilibration methods based on slowly changing the Hamiltonian parameters in the QMC simulation succeed in a polynomial time? We show that this is {\it not} true, by constructing counter-examples. In some examples, the space of configurations where the wavefunction has non-negligible amplitude has a nontrivial fundamental group, causing the space of trajectories in imaginary time to break into disconnected components with only negligible probability outside these components. For the simplest example we give with an abelian fundamental group, QMC does not equilibrate but still solves the optimization problem. More severe effects leading to failure to solve the optimization can occur when the fundamental group is a free group on two generators. Other examples where QMC fails have a {\it trivial} fundamental group, but still use ideas from topology relating group presentations to simplicial complexes. We define gadgets to realize these Hamiltonians as the effective low-energy dynamics of a transverse field Ising model. We present some analytic results on equilibration times which may be of some independent interest in the theory of equilibration of Markov chains. Conversely, we show that a small spectral gap implies slow equilibration at low temperature for some initial conditions and for a natural choice of local QMC updates.
Transcranial low-level laser therapy (810 nm) temporarily inhibits peripheral nociception: photoneuromodulation of glutamate receptors, prostatic acid phophatase, and adenosine triphosphate (2016)

Photobiomodulation or low-level light therapy has been shown to attenuate both acute and chronic pain, but the mechanism of action is not well understood. In most cases, the light is applied to the painful area, but in the present study we applied light to the head. We found that transcranial laser therapy (TLT) applied to mouse head with specific parameters (810 nm laser, [Formula: see text], 7.2 or [Formula: see text]) decreased the reaction to pain in the foot evoked either by pressure (von Frey filaments), cold, or inflammation (formalin injection) or in the tail (evoked by heat). The pain threshold increasing is maximum around 2 h after TLT, remains up to 6 h, and is finished 24 h after TLT. The mechanisms were investigated by quantification of adenosine triphosphate (ATP), immunofluorescence, and hematoxylin and eosin (H&E) staining of brain tissues. TLT increased ATP and prostatic acid phosphatase (an endogenous analgesic) and reduced the amount of glutamate receptor (mediating a neurotransmitter responsible for conducting nociceptive information). There was no change in the concentration of tubulin, a constituent of the cytoskeleton, and the H&E staining revealed no tissue damage. This is the first study to show inhibition of peripheral pain due to photobiomodulation of the central nervous system.
2021 Position Statement From the International Society for the Advancement of Spine Surgery on Cervical and Lumbar Disc Replacement (2021)

Cervical and lumbar degenerative disc disease are well-known causes of neck and back pain and associated radiculopathy in spine patients. The estimated 1-year incidence rate of neck pain and any episode of lower back pain is 10.4% to 21.3%[1][1],[2][2] and 1.5% to 36%,[3][3] respectively. Previous
High power transfer density and high efficiency 100 MHz capacitive wireless power transfer system (2015)

This paper introduces a very high frequency (VHF) capacitive wireless power transfer architecture capable of achieving very high power transfer densities and high efficiencies. High power density is achieved using an operating frequency of 100 MHz and through appropriate design of matching networks. High efficiency is achieved using a custom designed half-bridge GaN chip with integrated gate drivers. To validate performance of the proposed architecture, a prototype capacitive wireless power transfer system is built and tested. Experimental results demonstrate that the system transfers 2.5 W of power across a 1 pF capacitive interface at a very high power transfer density of 1.1 W/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , at close to 90% efficiency.
Toward a complete in silico , multi‐layered embryonic stem cell regulatory network (2010)

Recent efforts in systematically profiling embryonic stem (ES) cells have yielded a wealth of high-throughput data. Complementarily, emerging databases and computational tools facilitate ES cell studies and further pave the way toward the in silico reconstruction of regulatory networks encompassing multiple molecular layers. Here, we briefly survey databases, algorithms, and software tools used to organize and analyze high-throughput experimental data collected to study mammalian cellular systems with a focus on ES cells. The vision of using heterogeneous data to reconstruct a complete multi-layered ES cell regulatory network is discussed. This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low-throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature.
Catalytic Asymmetric Allylation of Aldehydes with Alkenes Mediated by Organophotoredox and Chiral Chromium Hybrid Catalysis (2018)

A hybrid system accomplishing cooperativity between an organophotoredox acridinium catalyst and a chiral chromium&lt;br&gt;complex catalyst was developed, enabling the unprecedented exploitation of unactivated hydrocarbon alkenes as precursors to chiral allylchromium nucleophiles for the asymmetric allylation of aldehydes. The reaction proceeded under visible light irradiation at room temperature and with high functional group tolerance, affording the corresponding homoallylic alcohols with up to &gt;20/1 diastereomeric ratio and 99% ee. The addition of Mg(ClO4)2 elicited profound enhancement of both reactivity and enantioselectivity.
Quantum Entropy Evolution (2021)

A quantum coordinate-entropy formulated in quantum phase space has been recently proposed together with an entropy law that asserts that such entropy can not decrease over time. The coordinate-entropy is dimensionless, a relativistic scalar, and it is invariant under coordinate and CPT transformations. We study here the time evolution of this entropy. We show that the entropy associated with coherent states evolving under a Dirac Hamiltonian is increasing. However, for the collisions of two particles, where each is evolving as a coherent state, as they come closer to each other their spatial entanglement causes the total system's entropy to oscillate. We augment time reversal with time translation and show that CPT with time translation can transform particles with decreasing entropy for a finite time interval into anti-particles with increasing entropy for the same finite time interval. We then analyze the impact of the entropy law for the evolution scenarios described above and explore the possibility that entropy oscillations trigger the annihilation and the creation of particles.
Disruption of long‐chain base hydroxylation alters growth and impacts sphingolipid synthesis in Physcomitrella patens (2021)

Sphingolipids have roles as membrane structural components and as bioactive molecules in plants. In <i>Physcomitrella patens</i>, 4-hydroxysphinganine (phytosphingosine, t18:0) is the predominant sphingolipid long-chain base (LCB). To assess the functional significance of t18:0, CRISPR-Cas9 mutagenesis was used to generate mutant lines lacking the sole <i>SPHINGOID BASE HYDROXYLASE</i> (<i>SBH</i>) gene encoding the hydroxylase responsible for converting sphinganine (d18:0) to t18:0. Total sphingolipid content in <i>sbh</i> protonemata was 2.4-fold higher than in wild-type. Modest changes in glycosyl inositolphosphorylceramide (GIPC) glycosylation patterns occurred. Sphingolipidomic analyses of mutants lacking t18:0 indicated modest alterations in acyl-chain pairing with d18:0 in GIPCs and ceramides, but dramatic alterations in acyl-chain pairing in glucosylceramides, in which 4,8-sphingadienine (d18:2) was the principal LCB. A striking accumulation of free and phosphorylated LCBs accompanied loss of the hydroxylase. The <i>sbh</i> lines exhibited altered morphology, including smaller chloronemal cell size, irregular cell shape, reduced gametophore size, and increased pigmentation. In the presence of the synthetic trihydroxy LCB t17:0, the endogenous sphingolipid content of <i>sbh</i> lines decreased to wild-type levels, and the mutants exhibited phenotypes more similar to wild-type plants. These results demonstrate the importance of sphingolipid content and composition to Physcomitrella growth. They also illuminate similarities in regulating sphingolipid content but differences in regulating sphingolipid species composition between the bryophyte <i>P. patens</i> and angiosperm <i>A. thaliana</i>.
Defective migration of neuroendocrine GnRH cells in human arrhinencephalic conditions (2010)

Patients with Kallmann syndrome (KS) have hypogonadotropic hypogonadism caused by a deficiency of gonadotropin-releasing hormone (GnRH) and a defective sense of smell related to olfactory bulb aplasia. Based on the findings in a fetus affected by the X chromosome–linked form of the disease, it has been suggested that hypogonadism in KS results from the failed embryonic migration of neuroendocrine GnRH1 cells from the nasal epithelium to the forebrain. We asked whether this singular observation might extend to other developmental disorders that also include arrhinencephaly. We therefore studied the location of GnRH1 cells in fetuses affected by different arrhinencephalic disorders, specifically X-linked KS, CHARGE syndrome, trisomy 13, and trisomy 18, using immunohistochemistry. Few or no neuroendocrine GnRH1 cells were detected in the preoptic and hypothalamic regions of all arrhinencephalic fetuses, whereas large numbers of these cells were present in control fetuses. In all arrhinencephalic fetuses, many GnRH1 cells were present in the frontonasal region, the first part of their migratory path, as were interrupted olfactory nerve fibers that formed bilateral neuromas. Our findings define a pathological sequence whereby a lack of migration of neuroendocrine GnRH cells stems from the primary embryonic failure of peripheral olfactory structures. This can occur either alone, as in isolated KS, or as part of a pleiotropic disease, such as CHARGE syndrome, trisomy 13, and trisomy 18.
New perspectives on the Semmler-Wolff aromatization reaction (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew perspectives on the Semmler-Wolff aromatization reactionMustafa I. El-Sheikh and James M. CookCite this: J. Org. Chem. 1980, 45, 13, 2585–2587Publication Date (Print):June 1, 1980Publication History Published online1 May 2002Published inissue 1 June 1980https://pubs.acs.org/doi/10.1021/jo01301a008https://doi.org/10.1021/jo01301a008research-articleACS PublicationsRequest reuse permissionsArticle Views538Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Expanding use of nonpenetrating clips in various surgical specialities. (2005)

The Anastoclip Vessel Closure System (VCS) (LeMaitre Vascular, Burlington, MA, USA), introduced primarily to facilitate microvascular anastomoses performed during neurosurgical extra-intracranial bypasses, has been used for several other applications as well. The relatively new anastomotic technique includes a clip applier, clip remover, and everting forceps. With the applier, tiny nonpenetrating titanium clips were installed on everted walls of tubular structures. The technical ease of application, reduced anastomotic time, superior hemodynamics, and an improved healing pattern at the anastomosis have been recognized as major advantages compared to conventional suturing. This chapter describes the various indications for use of the system and categorizes them by specific surgical specialties, which include neurosurgery, urology, and gynecology, as well as plastic and reconstructive, vascular, thoracic, transplantation, hepatopancreaticobiliary, and orthopedic and trauma surgery. The largest clinical experience with clips is in vascular access surgery for hemodialysis purposes, both in autologous constructs and with prosthetic grafts. Promising clinical results also have been achieved in neurosurgical cases (both for microvascular anastomoses and with closure of dura mater), microvascular free-tissue transfer, and renal and liver transplantations. Future clinical applications include the use of clips for nerve repair and closure of various types of tubular structures using a laparoscopic approach.
Analysis of ELF electromagnetic field pulses recorded by the Hylaty station coinciding with terrestrial gamma‐ray flashes (2012)

Terrestrial gamma‐ray flashes (TGFs) were registered the first time by the NASA's Compton Gamma Ray Observatory. The physical mechanism of TGF generation is not fully known, but there is a consensus among researchers that the radiation is produced by bremsstrahlung of relativistic electrons in the thunderstorm regions of the atmosphere. Therefore, TGFs have been linked to positive‐polarity intracloud lightning discharges, strong positive cloud‐to‐ground discharges or upward discharges from a thundercloud top. The currently operating Fermi Gamma‐ray Space Telescope is equipped with a Gamma‐ray Burst Monitor that can detect terrestrial gamma‐ray flashes. It opens up a new possibility to search for lightning discharges responsible for TGFs. Ground‐based lightning monitoring systems in the ELF, LF and VLF ranges can be used for that purpose. The ELF systems are especially useful, since they provide a large monitoring range of several thousand kilometers for strong atmospheric discharges (charge moments above several tens of C km). In this paper we have described the data analysis method for ELF electromagnetic field pulses and applied it to study our first examples of TGFs registered by Fermi GBM coinciding with ELF pulses recorded by the Hylaty ELF station located in the Carpathian Mountains in Poland. Using our ELF electromagnetic wave propagation model we have evaluated charge moments for the two registered events to be 320 and 110 C km and provided upper limits for the remaining events.
Entwicklung eines optischen 3-D-Positionsmeßsystems für die simultane Erfassung von 6 Freiheitsgraden / Development of an Optical RD Position Measuring System for the Simultaneous Determination of 6 Degrees of Freedom (2002)

A few years ago it became possible to carry out complicated surgical procedures in humans with the required precision by combining medical imaging (MRI, CT) with minimally invasive surgery. The confined space within these imaging systems and the resulting inaccuracies associated with the manual use of instruments increasingly make necessary the help of aids ranging from positioning systems to robotic devices, which themselves must be position controlled. A position sensor has been developed for a medical robotic system allowing the image-controlled insertion of injection needles and the simultaneous administration of different drugs. The 3D position coordinates are determined by a noncontact optical principle, which also enables simultaneous determination of all 6 basic degrees of freedom of the robotic system (3 translational, 3 rotational). On the basis of an area image sensor and the measurement of a geometrically defined structure in the path of the rays between sensor and light source, the position coordinates are calculated almost real time. Special emphasis was placed on designing the sensor system to cover a sufficiently large workspace to enable it to cover the entire intervention area. The sensor described herein determines the position coordinates in a volume of 10 x 10 x 10 cm at a resolution of up to 1 mm for translations and 1 degree for rotations.
Accuracy of 68Ga-PSMA11 PET/CT on recurrent prostate cancer: Preliminary results from a phase 2/3 prospective trial. (2018)

5001 Background: 68Ga-PSMA11 PET/CT provides improved localization of biochemically recurrent prostate cancer. For approval and reimbursement, accuracy needs to be established in a prospective study employing independent lesion validation. Methods: In this phase 2/3 prospective trial (NCT02940262), patients with biochemically recurrent prostate cancer after primary prostatectomy (n = 205) or radiation therapy (n = 45) underwent 68Ga-PSMA11 PET/CT. Presence of prostate cancer was recorded on a patient and region base. Regions were prostate bed, pelvis, extra-pelvic, and bone. Lesions were validated in 51% of PET/CT-positive patients by histopathology (n = 33), imaging (n = 62) and/or PSA after targeted radiation therapy (n = 9 patients). PSA response after 68Ga-PSMA11 PET/CT guided focal salvage therapy (surgery/radiotherapy) was recorded in 23 of 25 patients (8% drop out). Endpoints were positive predictive value (PPV), detection rate and outcome. Results: PPV validated by histopathology was 85% on a patient base (primary endpoint). PPV as determined by any type of validation was 89% on a patient and 91% on a region base. 68Ga-PSMA11 PET/CT localized recurrent prostate cancer in 197 of 250 (79%) patients; stratified by PSA: 41% for < 0.5 ng/ml (n = 54), 66% for 0.5 to < 1.0 ng/ml (n = 38), 86% for 1.0 to < 2.0 ng/ml (n = 36), 96% for 2.0 to < 5.0 ng/ml (n = 55), and 99% for ≥5.0 ng/ml (n = 67). Lesion location was in 35% prostate bed, 61% pelvis, 35% extra-pelvic, and 31% bone. Following focal salvage therapy alone, 18 (78%) patients had a PSA drop of 50% or more, 7 (30%) patients had biochemical complete response (PSA undetectable). Conclusions: Using an independent reference standard, we establish high 68Ga-PSMA11 PET/CT PPV for localization of recurrent prostate cancer. PET/CT guided salvage therapy resulted in high biochemical response rates. Pooled multicenter findings will be submitted for a New Drug Application. Clinical trial information: NCT02940262.
A transparent pricing scheme for interference mitigation in uplink OFDMA with collaborative distributed scheduling (2010)

Distributed uplink scheduling in a multicell OFDMA system is considered. A collaborative model is proposed, where base stations cooperate by exchanging interference information based on pricing, and users in each cell cooperate by exchanging channel state information. Then, each user implements independently the same scheduling algorithm. Simulations show that results close to the case of full channel knowledge can be achieved at the expense of a limited number of feedback bits per subcarrier. Furthermore, the proposed pricing scheme leads to enhanced results in the presence of interference.
A reference human induced pluripotent stem cell line for large-scale collaborative studies (2022)

Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.
Probing the substrate specificity of the dengue virus type 2 NS3 serine protease by using internally quenched fluorescent peptides (2006)

The NS3 (dengue virus non-structural protein 3) serine protease of dengue virus is an essential component for virus maturation, thus representing an attractive target for the development of antiviral drugs directed at the inhibition of polyprotein processing. In the present study, we have investigated determinants of substrate specificity of the dengue virus NS3 protease by using internally quenched fluorogenic peptides containing Abz (o-aminobenzoic acid; synonymous to anthranilic acid) and 3-nitrotyrosine (nY) representing both native and chimaeric polyprotein cleavage site sequences. By using this combinatorial approach, we were able to describe the substrate preferences and determinants of specificity for the dengue virus NS2B(H)-NS3pro protease. Kinetic parameters (kcat/K(m)) for the hydrolysis of peptide substrates with systematic truncations at the prime and non-prime side revealed a length preference for peptides spanning the P4-P3' residues, and the peptide Abz-RRRRSAGnY-amide based on the dengue virus capsid protein processing site was discovered as a novel and efficient substrate of the NS3 protease (kcat/K(m)=11087 M(-1) x s(-1)). Thus, while having confirmed the exclusive preference of the NS3 protease for basic residues at the P1 and P2 positions, we have also shown that the presence of basic amino acids at the P3 and P4 positions is a major specificity-determining feature of the dengue virus NS3 protease. Investigation of the substrate peptide Abz-KKQRAGVLnY-amide based on the NS2B/NS3 polyprotein cleavage site demonstrated an unexpected high degree of cleavage efficiency. Chimaeric peptides with combinations of prime and non-prime sequences spanning the P4-P4' positions of all five native polyprotein cleavage sites revealed a preponderant effect of non-prime side residues on the K(m) values, whereas variations at the prime side sequences had higher impact on kcat.