gebhart/patrepeval huggingface dataset:
Protein Pockets: Inventory, Shape, and Comparison (2010)

The shape of the protein surface dictates what interactions are possible with other macromolecules, but defining discrete pockets or possible interaction sites remains difficult. First, there is the problem of defining the extent of the pocket. Second, one has to characterize the shape of each pocket. Third, one needs to make quantitative comparisons between pockets on different proteins. An elegant solution to these problems is to sort all surface and solvent points by travel depth and then collect a hierarchical tree of pockets. The connectivity of the tree is determined via the deepest saddle points between each pair of neighboring pockets. The resulting pocket surfaces tessellate the entire protein surface, producing a complete inventory of pockets. This method of identifying pockets also allows one to easily compute important shape metrics, including the problematic pocket volume, surface area, and mouth size. Pockets are also annotated with their lining residue lists and polarity and with other residue-based properties. Using this tree and the various shape metrics pockets can be merged, grouped, or filtered for further analysis. Since this method includes the entire surface, it guarantees that any pocket of interest will be found among the output pockets, unlike all previous methods of pocket identification. The resulting hierarchy of pockets is easy to visualize and aids users in higher level analysis. Comparison of pockets is done by using the shape metrics, avoiding the complex shape alignment problem. Example applications show that the method facilitates pocket comparison along mutational or time-dependent series. Pockets from families of proteins can be examined using multiple pocket tree alignments to see how ligand binding sites or how other pockets have changed with evolution. Our method is called CLIPPERS for complete liberal inventory of protein pockets elucidating and reporting on shape.
Owlook Vaulting Taught Here (2010)

From the Rice Thresher Archive, a collection of newspaper articles published in the student newspaper for Rice University. Genre: News
Cell cycle dependence of foamy retrovirus infection (1995)

In common with oncoviruses but unlike the lentivirus human immunodeficiency virus type 1, foamy (spuma) viruses require host cell proliferation for productive infection. We show that human immunodeficiency virus type 1 replicates in RD-CD4 cells regardless of the growth arrest condition of the cells, while murine leukemia virus is unable to infect growth-arrested RD-CD4 cells or cells progressing through a partial cell cycle that includes S phase but not mitosis. Human foamy virus, like murine leukemia virus, does not productively infect G1/S or G2 growth-arrested cells. Two other foamy viruses, simian foamy virus type 1, isolated from a macaque, and simian foamy virus type 6, isolated from a chimpanzee, also fail to establish productive infection in G1/S-arrested cells.
Arguments against the role of cortical spreading depression in migraine (2018)

Cortical spreading depression (CSD) is a wave of increased electrocortical activity and vasodilation, followed by sustained decreased activity and prolonged vasoconstriction. Although the discovery of CSD has been ascribed to Leão, rather than vasoconstriction, he only observed a depression of neural activity combined with vasodilation, with much weaker stimulation than used by his followers. There is a longstanding belief that CSD underlies migraine aura, with its positive symptoms such as mosaic patterns and its negative symptoms such as scotoma, and a similar propagation speed and vasoreaction pattern. However, there are many arguments against this theory. CSD is difficult to evoke in man, and electroencephalography (EEG) readings are not flattened during migraine (as opposed to EEG during CSD). Moreover, in contrast to CSD, migraine can occur bilaterally, and is not accompanied by a disrupted blood-brain barrier, increased cerebral metabolism, or cerebral cell swelling. Calcitonin gene-related peptide, which is thought to be characteristic of migraine pain, is increased in the blood from the external jugular vein during migraine in humans, but not during CSD in cats or rats. Moreover, CSD does not explain the appearance of premonitory symptoms or allodynia, long before the actual onset of aura. In addition, there is a variation in the pain mechanisms of migraine and CSD, and in their reaction to transcranial magnetic stimulation and several pharmacologic interventions. Finally, the origin of putative CSD in migraine is currently unknown.
A drone with insect-inspired folding wings (2016)

Flying robots are increasingly adopted in search and rescue missions because of their capability to quickly collect and stream information from remote and dangerous areas. To further enhance their use, we are investigating the development of a new class of drones, foldable sensorized hubs that can quickly take off from rescuers' hands as soon as they are taken out of a pocket or a backpack. With this aim, this paper presents the development of a foldable wing inspired by insects. The wing can be packaged for transportation or deployed for flight in half a second with a simple action from the user. The wing is manufactured as a thick origami structure with a foldable multi-layer material. The prototype of the foldable wing is experimentally characterized and validated in flight on a mini-drone.
Thermoregulatory Sweat Test (2016)

The thermoregulatory sweat test (TST) consists of giving a controlled heat and humidity stimulus to produce a generalized sweat response. The TST assesses the integrity of efferent sympathetic sudomotor pathways. The entire anterior body surface is tested for both pre- and post-ganglionic lesions. The TST can evaluate patients with symptoms of small-fiber neuropathy and demonstrate autonomic involvement in disorders such as multiple system atrophy, hyperhidrosis, and some skin disorders. An indicator powder placed on the body surface before heating provides visualization of sweating and non-sweating skin. The patient’s weight (before and after heating) and height allows calculation of total body sweat rate, and the slope of the core temperature rise with time provides an estimate of heat tolerance. Normal and abnormal TST patterns, report generation, and difficulties and pitfalls in test interpretation are described.
Adaptive Base Station Cooperation for Physical Layer Security in Two-Cell Wireless Networks (2016)

We study physical layer security in two-cell wireless networks in which a base station (Alice) intends to send a confidential message to a legitimate user (Bob) with the help of a cooperative base station (Charlie), in the presence of an eavesdropper (Eve). Adaptive base station cooperation is explored to secure communication between Alice and Bob, and ensure the desired quality of service (QoS) at Charlie’s user. In particular, we consider two different scenarios where the channel state information of Eve is perfectly and statistically known, respectively. In either scenario, we provide a cooperative transmission scheme for secrecy rate maximization, subject to both security and QoS constraints. Unlike the conventional cooperative security with a fixed transmission scheme, we propose a mechanism for transmit strategy adaptation with security protection. Specifically, the cooperative transmission is replaced by a cooperative jamming scheme if either security or QoS constraint is not satisfied. Our design enables adaptive secure transmission, and thus is flexible and environment-adaptive. Moreover, numerical results confirm that our scheme is efficient in power resource utilization.
AMP-insensitive fructose bisphosphatase in Escherichia coli and its consequences. (1986)

Inhibition of fructose bisphosphatase (EC 3.1.3.11) by AMP is thought to be an important control mechanism, and, for the Escherichia coli enzyme, is the only control known. We here report on a mutant E. coli fructose bisphosphatase almost insensitive to this inhibition. The purified enzyme is normal in other respects. A strain with this enzyme instead of the wild-type enzyme grows normally in a variety of media. A strain with a very high level of the wild-type enzyme also grows normally. A strain with the very high level of mutant enzyme, however, does show growth abnormalities, but they are not clearly associated with the AMP insensitivity.
Space charge formation at the interface between a charge transport layer and a polyester film (1998)

The organic photoconductor structure used in a copying machine consists of electron-conductive and ion-conductive layers, a charge generation layer, and a charge transport layer. We applied the pulsed electroacoustic method, which has been used to evaluate HV insulation, to measure the space charge behavior of the charge transport layer coated on a polyester film. On the surface of the charge transport layer, various electrodes were evaporated. An internal space charge accumulated at the interface between the charge transport layer and the polyester film under a dc electric field. We show that the charge distribution is formed by the injection of holes from the anode and by the surface charge, and that the hole injection is influenced by the anode material.
Mechanism for photorefractive phase conjugation using incoherent beams (1988)

Two mutually incoherent extraordinary laser beams, incident upon opposite a faces of a BaTiO(3) crystal, generate a set of photorefractive holograms that channel both beams toward the +c face of the crystal, where they are internally reflected into the opposite channel. The resultant cross coupling of the two incident beams produces a pair of phase-conjugate (Phi*) beams. This new photorefractive interaction is characterized by reasonable Phi* reflectivities (~10-25%), good Phi* fidelity, and no image cross talk. The variations in Phi* reflectivity with crystal orientation, angles of incidence, and intensity ratio are presented. The formation times of the photorefractive gratings responsible for the phase conjugation are significantly shorter than those of other self-pumped phase conjugators.
Genes Involved in Differentiation, Stem Cell Renewal, and Tumorigenesis Are Modulated in Telomerase-Immortalized Human Urothelial Cells (2008)

The expression of hTERT, the catalytic subunit of telomerase, immortalizes normal human urothelial cells (NHUC). Expression of a modified hTERT, without the ability to act in telomere maintenance, did not immortalize NHUC, confirming that effects at telomeres are required for urothelial immortalization. Previous studies indicate that inhibition of telomerase has an immediate effect on urothelial carcinoma (UC) cell line viability, before sufficient divisions to account for telomere attrition, implicating non-telomere effects of telomerase in UC. We analyzed the effects of telomerase on gene expression in isogenic mortal and hTERT-transduced NHUC. hTERT expression led to consistent alterations in the expression of genes predicted to be of phenotypic significance in tumorigenesis. A subset of expression changes were detected soon after transduction with hTERT and persisted with continued culture. These genes (NME5, PSCA, TSPYL5, LY75, IGFBP2, IGF2, CEACAM6, XG, NOX5, KAL1, and HPGD) include eight previously identified as polycomb group targets. TERT-NHUC showed overexpression of the polycomb repressor complex (PRC1 and PRC4) components, BMI1 and SIRT1, and down-regulation of multiple PRC targets and genes associated with differentiation. TERT-NHUC at 100 population doublings, but not soon after transduction, showed increased saturation density and an attenuated differentiation response, indicating that these are not acute effects of telomerase expression. Some of the changes in gene expression identified may contribute to tumorigenesis. Expression of NME5 and NDN was down-regulated in UC cell lines and tumors. Our data supports the concept of both telomere-based and non-telomere effects of telomerase and provides further rationale for the use of telomerase inhibitors in UC.
Electrowetting Properties of ZnO and TiO<sub>2</sub> Nanostructured Thin Films (2010)

Electrowetting experiments have been performed on ZnO and TiO2 nanostructured thin films grown on crystalline Si and subsequently coated by a thin dielectric layer. The contact angle is decreased upon the application of an electric field between the film and a water droplet placed on the dielectric surface until saturation is observed. The electrowetting phenomenon is reversible, with the droplet returning to its initial hydrophobic state, when the applied potential is decreased. For the actuation of the droplet, low voltage, on the order of a few volts, is required.
Fibrinogen adsorption and platelet lysis characterization of fluorinated surface‐modified polyetherurethanes (2006)

A polyetherurethane (PU) was modified using fluorinated surface-modifying macromolecules (SMMs). A double radiolabel method was used simultaneously to measure the number of adhered platelets ((51)Cr) and the quantity of adsorbed Fg ((125)I), in a cone-and-plate instrument. The objectives were to determine if adsorbed Fg levels correlated to platelet adhesion on the surfaces, and to assess if any reductions in platelet adhesion for the SMM-treated surfaces resulted from surface-induced platelet lysis, rather than changes directly related to lower platelet activation and attachment on the novel surfaces. Platelet lysis was determined from lactate dehydrogenase (LDH) and unbound (51)Cr released into plasma isolated from whole blood exposed to test materials. The corresponding Fg adsorption, evaluated under the same platelet adhesion conditions, did not account for the reduced platelet adhesion on the treated surfaces. LDH and (51)Cr platelet release were very low and indicated no statistically significant differences between the materials. It was therefore concluded that platelet lysis did not contribute to the reduction in platelet adhesion characteristic observed on the SMM-treated surfaces. More importantly, the work emphasizes that the platelet activation cannot be inferred to by assessing the quantity of fibrinogen as is commonly done in the literature. The finding suggests a much more complex mechanism of action for the SMM surface modifiers. On-going work is investigating other Fg parameters such as protein binding affinity and protein conformational state in order to establish the mechanism by which the fluorinated surface modifiers may be reducing platelet adhesion via intermediary changes in initial protein adsorption.
Enzymic hydrolysis of alkyl 3,4-epoxybutyrates. A new route to (R)-(-)-carnitine chloride (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic hydrolysis of alkyl 3,4-epoxybutyrates. A new route to (R)-(-)-carnitine chlorideDaniele Bianchi, Walter Cabri, Pietro Cesti, Franco Francalanci, and Marco RicciCite this: J. Org. Chem. 1988, 53, 1, 104–107Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/jo00236a021https://doi.org/10.1021/jo00236a021research-articleACS PublicationsRequest reuse permissionsArticle Views291Altmetric-Citations49LEARN 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
High efficiency PERT cells on n-type silicon substrates (2003)

High minority carrier lifetimes of a few milliseconds have been demonstrated both on CZ and FZ n-type silicon substrates. It is particularly interesting that the phosphorus doped n-type CZ wafers give minority carrier lifetimes nearly as high as those from the best p-type FZ silicon materials. This gives a good potential for very high performance on n-type CZ substrates. 21.1% and 21.9% efficiencies are reported for PERT (passivated emitter, rear totally-diffused) cells fabricated on these n-type mono-crystalline CZ and FZ silicon substrates, respectively. High open-circuit voltages approaching 700 mV have been demonstrated by these cells. Unfortunately, a non-uniform emitter saturation current has caused low fill factors for these cells, which will be investigated in future research.
Surgical preconditioning and completion of total cavopulmonary connection by interventional cardiac catheterisation: a new concept. (1996)

A new, staged procedure for univentricular repair of "high risk" patients using a combined surgical transcatheter technique is reported. As first step a surgical hemifontan procedure was performed and a multifenestrated patch inserted into the right atrium. For later transcatheter completion of univentricular repair, a subtotal banding just above the cavoatrial junction was performed. Two months later transcatheter completion was performed by balloon dilatation of the banded cavo-atrial junction and additionally either by inserting a covered stent as intracardiac conduit between the superior and inferior vena cava or by inserting a (non-covered) stent into the cavo-atrial junction and occluding the fenestrations in the right atrial patch using Rashkind-PDA occluders. This new technique was successfully applied without mortality in eight patients with a preoperative mean pulmonary pressure of 18 to 23 mm Hg. No complications typical for Fontan-like corrections occurred within the follow up period of 4 to 14 months.
Frozen‐section services by telepathology: Experience of 100 cases in the San‐in District, Japan (1996)

The early experience is reported here of the use of intra-operative frozen-section service by telepathology using the integrated Service Digital Network (ISDN), a commercially available system that is being connected between the Department of Pathology of Tottori University and Matsue City Hospital, a distance of 30 km. The transfer rate is currently 64 kbit/s. The frozen-section service was conducted for a total of 117 tissue specimens (organs) from 100 patients between August 1993 and May 1995. The average time taken for examination of each specimen of frozen section was 13 min, ranging between 2 and 42 min. The average number of transmitted images was 6.2. Six cases necessitated more than 11 transmitted images to make a diagnosis, while 13 cases could be diagnosed from two images only. Correct and permissible diagnoses were obtained in 109 (93.2%) out of 117 specimens when comparing the telepathology diagnosis with that of direct microscopy. Improper or misdiagnosis was made for eight cases (specimens), which were misinterpreted as papillary carcinoma in Basedow's disease, adenoma and hyperplasia in two pheochromocytomas, solid-tubular carcinoma in phyllodes tumor, mastopathy in invasive carcinoma, metastatic carcinoma in astrocytoma, follicular lymphoma in reactive hyperplasia, and lymphadenitis in follicular lymphoma. In retrospect, diagnosis of these cases should have been deferred. From the results, it was concluded that the intraoperative frozen-section service by telepathology may be a worthwhile substitute for hospitals with limited accessibility to local pathology service, in spite of pitfalls in some cases. Well prepared, high-quality frozen section, sufficient verbal communication with surgeons, and a rather conservative attitude on the part of a well-trained pathologist seem to be the essential ingredients for reaching an accurate decision when using telepathology.
Testing and Modeling of Shock Mitigating Seats for High Speed Craft (2011)

This study conducted a series of tests on a shock mitigating seat designed for high speed craft using various input excitations to better understand the relationship between various seat and operational conditions, and the response of the seat. A seat model of the test seat is used for a parametric study of various spring, damping and operational configurations. A seat shake rig is implemented to simulate motions of multiple high-speed craft as well as various defined inputs. At each test input the occupant weight and suspension preload is varied and the response is analyzed to find changes in acceleration, which is representative of the changes in force and displacement. By representing the seat as a based-excitation two-degree-of-freedom system, we develop the equations of motion and model them in Simulink to analyze the effects of various spring rates and damping coefficients. Based on the results it is found that an increase in occupant mass results in a decrease in observed acceleration. Increasing suspension preload is found to be detrimental to the mitigating abilities of the seat, changing the dynamics to those similar of a rigid-mounted seat. An analysis of the defined inputs resulted in confirming various seat characteristics. The analysis of the Simulink model revealed that increasing the spring rate results in an increase in acceleration. An increase in damping coefficient resulted in an increase in acceleration and ride harshness.
Nanoscale Engineering of a Cellular Interface with Semiconductor Nanoparticle Films for Photoelectric Stimulation of Neurons (2006)

The remarkable optical and electrical properties of nanostructured materials are considered now as a source for a variety of biomaterials, biosensing, and cell interface applications. In this study, we report the first example of hybrid bionanodevice where absorption of light by thin films of quantum confined semiconductor nanoparticles of HgTe produced by the layer-by-layer assembly stimulate adherent neural cells via a sequence of photochemical and charge-transfer reactions. We also demonstrate an example of nanoscale engineering of the material driven by biological functionalities.
High voltage gain CMOS OTA for micropower SC filters (1981)

The letter describes a single stage operational transconductance amplifier (OTA) with cascoded output transistors, designed for micropower switched-capacitor filters. The device features high voltage gain (>90 dB) under capacitive load, large output swing, very low power consumption (5 μW at 3 V supply voltage for 100 kHz bandwidth with 10 pF load) and reduced circuit area (<0.1 mm2).
Leukocyte migration inhibition in vitro in bladder carcinoma. (1979)

The leukocyte migration inhibition response in vitro of peripheral blood leukocytes from patients with transitional cell carcinoma of the urinary bladder, other genitourinary diseases, and normal controls was studied. The agarose droplet migration inhibition method was used to determine the cell-mediated immune reactivity of bladder tumor patients to antigens derived from allogeneic bladder tumor cell lines by hypertonic potassium chloride extraction. Sixty-nine bladder tumor patients were tested 131 times and included 68 positive and 63 negative results. A positive assay was shown to correlate strongly with the presence of tumor at the time of testing (p less than 0.001). Five of 24 patients with other genitourinary diseases had positive inhibition assays, but none of the 26 normal controls were positive. These results suggest that this in vitro assay method may prove valuable in monitoring bladder tumor patients for completeness of initial tumor resection and for clinical recurrence as well as for further studies of the tumor-specific immune response in this disease.