gebhart/patrepeval huggingface dataset:
Novel ALD Chemistry Enabled Low-Temperature Synthesis of Lithium Fluoride Coatings for Durable Lithium Anodes (2018)

Lithium metal anodes can largely enhance the energy density of rechargeable batteries because of the high theoretical capacity and the high negative potential. However, the problem of lithium dendrite formation and low Coulombic efficiency (CE) during electrochemical cycling must be solved before lithium anodes can be widely deployed. Herein, a new atomic layer deposition (ALD) chemistry to realize the low-temperature synthesis of homogeneous and stoichiometric lithium fluoride (LiF) is reported, which then for the first time, as far as we know, is deposited directly onto lithium metal. The LiF preparation is performed at 150 °C yielding 0.8 Å/cycle. The LiF films are found to be crystalline, highly conformal, and stoichiometric with purity levels >99%. Nanoindentation measurements demonstrate the LiF achieving a shear modulus of 58 GPa, 7 times higher than the sufficient value to resist lithium dendrites. When used as the protective coating on lithium, it enables a stable Coulombic efficiency as high as 99.5% for over 170 cycles, about 4 times longer than that of bare lithium anodes. The remarkable battery performance is attributed to the nanosized LiF that serves two critical functions simultaneously: (1) the high dielectric value creates a uniform current distribution for excellent lithium stripping/plating and ultrahigh mechanical strength to suppress lithium dendrites; (2) the great stability and electrolyte isolation by the pure LiF on lithium prevents parasitic reactions for a much improved CE. This new ALD chemistry for conformal LiF not only offers a promising avenue to implement lithium metal anodes for high-capacity batteries but also paves the way for future studies to investigate failure and evolution mechanisms of solid electrolyte interphase (SEI) using our LiF on anodes such as graphite, silicon, and lithium.
Silicon Growth at the Two-Dimensional Limit on Ag(111) (2014)

Having fueled the microelectronics industry for over 50 years, silicon is arguably the most studied and influential semiconductor. With the recent emergence of two-dimensional (2D) materials (e.g., graphene, MoS2, phosphorene, etc.), it is natural to contemplate the behavior of Si in the 2D limit. Guided by atomic-scale studies utilizing ultrahigh vacuum (UHV), scanning tunneling microscopy (STM), and spectroscopy (STS), we have investigated the 2D limits of Si growth on Ag(111). In contrast to previous reports of a distinct sp(2)-bonded silicene allotrope, we observe the evolution of apparent surface alloys (ordered 2D silicon-Ag surface phases), which culminate in the precipitation of crystalline, sp(3)-bonded Si(111) nanosheets. These nanosheets are capped with a √3 honeycomb phase that is isostructural to a √3 honeycomb-chained-trimer (HCT) reconstruction of Ag on Si(111). Further investigations reveal evidence for silicon intermixing with the Ag(111) substrate followed by surface precipitation of crystalline, sp(3)-bonded silicon nanosheets. These conclusions are corroborated by ex situ atomic force microscopy (AFM), transmission electron microscopy (TEM), Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS). Even at the 2D limit, scanning tunneling spectroscopy shows that the sp(3)-bonded silicon nanosheets exhibit semiconducting electronic properties.
Author response: Automated cell-type classification in intact tissues by single-cell molecular profiling (2017)

The ability to rapidly stain for any combination of genes in intact tissue with automated quantification of transcripts in individual cells and spatial re-mapping affords new insights into lung biology, and will greatly accelerate progress in scientific and medical research.
Fast geometric approximation techniques and geometric embedding problems (1989)

Given an undirected n-vertex graph G and a set of n points in Rd, we wish to embed the vertices of G onto the points so as to minimize the total embedded edge length. Important special cases of this geometric embedding problem are those in which G is a binary tree, a cycle, or a star. We give fast approximation algorithms for embedding these graphs on the line and in the plane in several metrics. Our principal techniques are: a notion of “approximate geometric sorting” that can be computed in linear time, and fast approximation schemes for the minimum spanning tree problem in the plane. We expect that these approximation techniques can be applied to many geometric problems besides the embedding problem. We give the example of approximating the convex hull of a set of points in the plane.
Synthetic Lethality in Lung Cancer—From the Perspective of Cancer Genomics (2019)

Cancer is a genetic disease, and this concept is now widely exploited by both scientists and clinicians to develop new genotype-selective anticancer therapeutics. Although the quest of cancer genomics is in its dawn, recognition of the widespread applicability of genetic interactions with biological processes of tumorigenesis is propelling research throughout academic fields. Lung cancer is the most common cause of cancer death worldwide, with an estimated 1.6 million deaths each year. Despite the development of targeted therapies that inhibit oncogenic mutations of lung cancer cases, continued research into new therapeutic approaches is required for untreatable lung cancer patients, and the development of therapeutic modalities has proven elusive. The "synthetic lethal" approach holds the promise of delivering a therapeutic regimen that preferentially targets malignant cells while sparing normal cells. We highlight the potential challenges in synthetic lethal anticancer therapeutics that target untreatable genetic alterations in lung cancer. We also discuss both challenges and opportunities regarding the application of new synthetic lethal interactions in lung cancer.
Design of vibration suppression controller for 3-inertia systems using Taguchi method (2006)

This paper presents a novel vibration suppression method for a 3-inertia control system by a modified-IPD (integral plus proportional plus derivative) controller. In the IPD structure, the integral action integrates the error between the designed output and the plant output, and the proportional and derivative terms act on the plant output only. The modified form introduces one extra parameter for added flexibility. We apply the Taguchi method for the determination of the controller gains. The effectiveness of the method is verified by simulations
Optimization of Activity, Selectivity, and Liability Profiles in 5-Oxopyrrolopyridine DPP4 Inhibitors Leading to Clinical Candidate (Sa)-2-(3-(Aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-5-oxo-5H-pyrrolo[3,4-b]pyridin-6(7H)-yl)-N,N-dimethylacetamide (BMS-767778) (2013)

Optimization of a 5-oxopyrrolopyridine series based upon structure-activity relationships (SARs) developed from our previous efforts on a number of related bicyclic series yielded compound 2s (BMS-767778) with an overall activity, selectivity, efficacy, PK, and developability profile suitable for progression into the clinic. SAR in the series and characterization of 2s are described.
Podocytes are lost from glomeruli before completing apoptosis (2022)

Although apoptosis of podocytes has been widely reported in in vitro studies, it has been less frequently and less definitively documented in in vivo situations. To investigate this discrepancy, we analyzed the dying process of podocytes in vitro and in vivo using LMB2, a human (h)CD25-directed immunotoxin. LMB2 induced cell death within 2 days in 56.8 ± 13.6% of cultured podocytes expressing hCD25 in a caspase-3, Bak1, and Bax-dependent manner. LMB2 induced typical apoptotic features, including TUNEL staining and fragmented nuclei without lactate dehydrogenase leakage. In vivo, LMB2 effectively eliminated hCD25-expressing podocytes in NEP25 mice. Podocytes injured by LMB2 were occasionally stained for cleaved caspase-3 and cleaved lamin A but never for TUNEL. Urinary sediment contained TUNEL-positive podocytes. To examine the effect of glomerular filtration, we performed unilateral ureteral obstruction in NEP25 mice treated with LMB2 1 day before euthanasia. In the obstructed kidney, glomeruli contained significantly more cleaved lamin A-positive podocytes than those in the contralateral kidney (50.1 ± 5.4% vs. 29.3 ± 4.1%, <i>P</i> < 0.001). To further examine the dying process without glomerular filtration, we treated kidney organoids generated from nephron progenitor cells of NEP25 mice with LMB2. Podocytes showed TUNEL staining and nuclear fragmentation. These results indicate that on activation of apoptotic caspases, podocytes are detached and lost in the urine before nuclear fragmentation and that the physical force of glomerular filtration facilitates detachment. This phenomenon may be the reason why definitive apoptosis is not observed in podocytes in vivo.<b>NEW & NOTEWORTHY</b> This report clarifies why morphologically definitive apoptosis is not observed in podocytes in vivo. When caspase-3 is activated in podocytes, these cells are immediately detached from the glomerulus and lost in the urine before DNA fragmentation occurs. Detachment is facilitated by glomerular filtration. This phenomenon explains why podocytes in vivo rarely show TUNEL staining and never apoptotic bodies.
Centralized Rainfall Estimation Using Carrier to Noise of Satellite Communication Links (2018)

In this paper, we present a centralized method for real-time rainfall estimation using carrier-to-noise power ratio ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$C/N$ </tex-math></inline-formula> ) measurements from broadband satellite communication networks. The <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$C/N$ </tex-math></inline-formula> data of both forward link and return link are collected by the gateway station from the user terminals in the broadband satellite communication network and stored in a database. The <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$C/N$ </tex-math></inline-formula> for such Ka-band scenarios is impaired mainly by the rainfall. Using signal processing and machine learning techniques, we develop an algorithm for real-time rainfall estimation. Extracting relevant features from <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$C/N$ </tex-math></inline-formula> , we use artificial neural network in order to distinguish the rain events from dry events. We then determine the signal attenuation corresponding to the rain events and examine an empirical relationship between rainfall rate and signal attenuation. Experimental results are promising and prove the high potential of satellite communication links for real environment monitoring, particularly rainfall estimation.
Highly Efficient Self‐Healing Multifunctional Dressing with Antibacterial Activity for Sutureless Wound Closure and Infected Wound Monitoring (Adv. Mater. 3/2022) (2022)

Wound Healing In article number 2106842, Miaomiao Yuan, Daxiang Cui, Hossam Haick, and co-workers report a novel self-healing elastomer-based multifunctional wound dressing (MFWD) with desirable mechanical robustness, biocompatibility, and antibacterial activity for effective wound management. MFWD assists in contracting wound edges, based on the excellent self-healing ability of the elastomer, and enables tracking of the wound health status in real-time via a set of (bio)chemical and physical sensors integrated therein.
Supplementary movie 4 from Serine-Threonine Kinase TAO3-Mediated Trafficking of Endosomes Containing the Invadopodia Scaffold TKS5α Promotes Cancer Invasion and Tumor Growth (2023)

&lt;p&gt;Effect of SU11333 on TKS5alpha vesicle trafficking&lt;/p&gt;
Assessing Changes in Texture Periodicity Due to Appearance Loss in Carpets: Gray Level Co-occurrence Analysis (1991)

Texture may be defined with respect to the global properties of an image or to the repeating units that compose it. We have attempted to isolate the periodic components of texture in wool carpets for the purpose of assessing the effects of wear on carpet textures. Texture is defined as any recurring spatial pattern of sampled gray level intensities. We restrict attention to textural features that reflect the physical charac teristics of the carpet tuft assemblies. Our test materials consist of four kinds of double ply wool carpets of differing textures divided into control, light, and heavy wear samples. Video images were recorded under several magnifications using a Truevision Vista board. Image files with 256 gray levels were converted to 32 levels using histogram equalization. Textural features were evaluated by computing gray level differences and second-order gray level statistics. We discuss results for spatial gray level depen dence (SGLDM) and gray level difference (GLDM) methods for a range of intersam pling distances. Results for our carpet series show that SGLDM and GLDM yield very similar trends, statistical trends within each method are correlated, overall, these mea sures are generally effective for differentiating the degree of wear as well as providing an indication of textural periodicity, and changes in frequency may be examined by subjecting SGLDM and GLDM statistics to spectral analysis.
Outgassing Properties of Chemically Polished Stainless Steels. (1998)

Chemical polishing (CP) was selected to develop a practical surface treatment of stainless steel that will be generally used in ultrahigh vacuum (UHV) technology because CP can treat materials wholly in any shape at the final step of parts fabrication process.Using short samples of SUS304L stainless steel the solution and the polishing condition were optimized from outgassing rate and reproducibility. The polished surfaces were characterized by Auger electron spectroscopy (AES), scanning electron microscopy (SEM), and Atomic force microscopy (AFM).The chemically polished (CP) chamber was compared with those treated by conventional electrolytic polishing (EP) and glass beads blasting (GBB). In pump-down curves, the outgassing rate of CP samples was the same as that of EP one and 10% of GBB one. At the ultimate pressure at 28°C after 150°C × 20 h baking the outgassing rate of the three chambers with different surface treatments showed a same value, 1 × 10-9 Pa·m·s-1.The technical purpose to use the CP for UHV material surface treatment is satisfied by this result and the cost of CP is less than that of EP because it doesn't need electricity.
Efficient color mixing through étendue conservation using freeform optics (2015)

Today’s SSL illumination market shows a clear trend to high flux packages with higher efficiency and higher CRI, realized by means of multiple color chips and phosphors. Such light sources require the optics to provide both near- and far-field color mixing. This design problem is particularly challenging for collimated luminaries, since traditional diffusers cannot be employed without enlarging the exit aperture and reducing brightness. Furthermore, diffusers compromise the light output ratio (efficiency) of the lamps to which they are applied. A solution, based on Köhler integration, consisting of a spherical cap comprising spherical microlenses on both its interior and exterior sides was presented in 2012. The diameter of this so-called Shell-Mixer was 3 times that of the chip array footprint. A new version of the Shell-Mixer, based on the Edge Ray Principle and conservation of etendue, where neither the outer shape of the cap nor the surfaces of the lenses are constrained to spheres or 2D Cartesian ovals will be shown in this work. The new shell is freeform, only twice as large as the original chip-array and equals the original model in terms of color uniformity, brightness and efficiency.
Supplementary Figure 3 from Canonical Wnt Signaling Is Required for Pancreatic Carcinogenesis (2023)

&lt;p&gt;PDF file - 879K, Supplemental Figure 3. PAS, Gomori Trichrome and Claudin18 IHC staining in KC and KDC pancreas.&lt;/p&gt;
Quantifying the potential of C-11 acetate PET scanning in avanced prostate cancer patients. (2016)

300 Background: Detection of advanced prostate cancer has historically relied on radionuclide bone scanning and cross-sectional imaging with varying degrees of sensitivity and specificity based on the clinical scenario. In the current era, use of NaF and Choline based whole body scans have led to increased detection, but access to these scan can be limited and expense can be prohibitive. Similar to choline based scanning, acetate is metabolically active in cancer, including prostate. Methods: Fifty-six men previously diagnosed with prostate cancer with PSA recurrences after some failed primary treatment, have undergone whole body C-11 Acetate PET scans at Indiana University since June of 2013. Patient demographics, prior treatments, PSA values, prior imaging, post-scan therapies, and therapeutic outcomes have been recorded prospectively and updated as follow-up information becomes available. Results: Analysis of these initial 56 men demonstrated 31/56 men had a C-11 Acetate PET scan that lead to further definitive loco-regional treatments, including salvage radiation therapy ( 12), salvage regional lymph node dissection (11) and salvage cryo-ablation (8), while 9/56 men had initiation of hormonal ablation, secondary to detection of systemic disease. The remainder of these men had negative scans and are currently under continued active surveillance without evidence of disease progression requiring either loco-regional or systemic therapy. Closer analysis of the 31 men who received loco-regional treatments revealed 10 men who benefited with clear PSA declines, 4 men who failed to demonstrate a benefit from the definitive loco-regional therapy and 17 of men are too early to determine at the time of analysis. Careful pathological analysis of the regional lymph dissections revealed the limit of detection of the C-11 Acetate PET scan of greater than or equal to 3mm. Correlations of SUV readings of detected prostate cancer lesions with PSA kinetics, suggest importance of both PSA doubling time and absolute PSA value cutoffs. Conclusions: The C-11 Acetate PET scan is a useful adjunct to current imagining techniques and provides additional clinical information to guide clinicians caring for prostate cancer patients.
Enantioselective, protecting group-free synthesis of 1S-ethyl-4-substituted quinolizidines (2012)

A practical enantioselective protecting group-free four-step route to the key quinolizidinone 6 from phenylglycinol-derived bicyclic lactam 1 is reported. The Grignard addition reaction to 6 takes place stereoselectively to give 1-ethyl-4-substituted quinolizidines 4-epi-207I and 7-9. Following a similar synthetic sequence, 9a-epi-6 is also accessed. However, the addition of Grignard reagents to 9a-epi-6 proceeds in a non-stereoselective manner. In order to gain insight into the different stereochemical outcome in the two series, theoretical calculations on the iminium salts A and B have been performed. The study concludes that the addition of the hydride, which is the step that determines the configuration of the final products, occurs in a stereoelectronic controlled manner. The theoretical study is in agreement with the experimental results.
Studies on the intraperitoneal Infection of Staphylococci in mice (1963)

In the present studies on the intraperitoneal infection of staphylococci in mice, virulence enhancement with gastric mucin and immune effects of staphylococcal a-toxoid in the case of intraperitoneal challenge by staphylococci with mucin were investigated and the following results were obtained:1. LD50in the intraperitoneal inoculation of staphylococci freshly isolated from supprative lesions decreased by addition of 0.2-0.2 ml of 5% gastric mucin suspension.2. The degree of the decrease of LD50by addition of mucin was not always connected with the coagulase production of the strains. And the decrease was remarkable in the Smith strain etc., but not in the Terajima strain which was preserved for a long time.3. Mice inoculated intraperitoneally with staphylococci and mucin were killed by septicemia, and the bacterial amounts in organs such as kidney, spleen, liver, heart and lung increased far more than those in the injection of the cocci without mucin.4. Most of mice intraperitoneally challenged as above died in an earlier stage. The number of bacteria of various organs was measured at intervals after the inoculation and proved to be different in the course of time by the difference of strains and organs, but the increase of number could be recognized about four hours after the inoculation in every case.5. Intraperitoneal challenge of staphylococci with mucin was found to be a useful method for the observation of immune effects of staphylococcal a-toxoid.6. In addition to the immune effects, the appearance of hypersensitiveness in mice by staphylococcalα-toxoids could also be demonstrated by these intraperitoneal challenge.
The Sjogren’s Syndrome-Associated Autoantigen Ro52 Is an E3 Ligase That Regulates Proliferation and Cell Death (2006)

Patients affected by Sjögren's syndrome and systemic lupus erythematosus (SLE) carry autoantibodies to an intracellular protein denoted Ro52. Although the serologic presence of Ro52 autoantibodies is used clinically for diagnostic purposes, the function of the protein or why it is targeted as an autoantigen in several rheumatic conditions has not been elucidated. In this study, we show that the expression of Ro52 is significantly increased in PBMC of patients with Sjögren's syndrome and SLE, and demonstrate that Ro52 is a RING-dependent E3 ligase involved in ubiquitination. Overexpression of Ro52, but not of Ro52 lacking the RING domain, in a mouse B cell line lead to decreased growth in steady state and increased cell death after activation via the CD40 pathway. The role of Ro52 in activation-mediated cell death was further confirmed as a reduction in Ro52 expression restored cell viability. These findings suggest that the increased expression of the Ro52 autoantigen in patients may be directly involved in the reduced cellular proliferation and increased apoptotic cell death observed in Sjögren's syndrome and SLE, and may thus contribute to the autoantigenic load and induction of autoimmune B and T cell responses observed in rheumatic patients.
Bordetella avium: An Opportunistic Pathogen in Leghorn Chickens (1995)

Experiments were conducted in order to produce bordetellosis in specific-pathogen-free (SPF) leghorn chickens. In the first and second of three experiments, young turkeys and chickens, respectively, were allotted into groups and challenged at 2 weeks of age with one of seven different isolates of Bordetella avium and two isolates of B. avium-like bacteria. Isolates of B. avium with the smooth colony type were pathogenic in turkeys but not in chickens. The B. avium-like bacteria and B. avium isolates with rough colonial morphology were nonpathogenic. In the third experiment, SPF leghorn chicks were vaccinated at 1 day of age with infectious bronchitis virus, Newcastle disease virus, or both and then challenged with B. avium at 7 days of age. Chickens vaccinated and then challenged with B. avium showed clinical signs and lesions similar to bordetellosis in turkeys. No clinical signs were observed in unchallenged chickens. Thus, we conclude that B. avium is an opportunistic pathogen in SPF leghorn chickens.
Supplemental File 2 from Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (2023)

&lt;p&gt;The script for ChIP-Seq and RNA-Seq data integration&lt;/p&gt;