gebhart/patrepeval huggingface dataset:
Surface and Volume Changes in the Lens during Accommodation (2011)

I was excited by the results presented in the excellent paper by Sheppard et al. I was very gratified that they acknowledged that we had predicted similar changes in human lens volume and surface based on mathematical modeling of human lens dimensions, using the Pappus theorem as well as our experimentally induced changes in lens dimensions of isolated cow lenses under conditions mimicking accommodation. heir acknowledgment of our work is especially gratifying for us because members of the "accommodation group" had received our findings and predictions with skepticism. I hope that the publication by Sheppard et al. serves to encourage a reevaluation of the changes that occur during accommodation.
Housing Administration Building - 031 (2005)

Housing Administration Building (Bldg 031)\nCompletion Date: 2007\nSquare Feet: 8,360\nArchitect: Rebecca L. Binder, F.A.I.A.\nCal Poly President: Warren J. Baker (1979-Present)
Supplementary Figures and legends from Carbonic Anhydrase XII Inhibitors Overcome P-Glycoprotein–Mediated Resistance to Temozolomide in Glioblastoma (2023)

&lt;p&gt;The file contains Supplementary Figure S1-S6: Figure S1 shows Pgp and CAXII expression in different culture conditions; Figure S2 shows the effects of compounds 1-5 on chemotherapeutic drugs cytotoxicity; Figure S3 shows the effects of compound 1 and temozolomide in Pgp KO clones; Figure S4 shows isobologram analysis; Figure S5 shows CAXII-KO clones; Figure S6 shows AC and NS tumor growth with different dosing of compound 1 and temozolomide.&lt;/p&gt;
Influences of Ventricular Assist Device Pumping on Blood Coagulation (1989)

A left ventricular assist device (VAD) with a smooth surface of segmented polyurethane was implanted in five goats for 10–55 days, and plasma levels of fibrinogen (Fg), prekallikrein (PK), fibrinogen, fibrin degradation products (FDP), antithrombin III (AT III), prothrombin time (PT), partial thromboplastin time (PTT), platelet (PI) count, and platelet aggregation (PlAg) induced by adenosine diphosphate were measured during the experiment. Heparin was administered during surgery and no systemic antithrombotic therapy was given thereafter. Before the third postoperative day (POD), plasma levels of Fg and PK were at their lowest, and increased afterward. Between the second and fifth POD PT and PTT increased to 130–160%, and returned to normal gradually. Plasma FDP appeared on the second POD and reached peak values of 10–40 μg/ml on the sixth POD. Platelet and AT III levels showed no uniform tendency, but the rate of PlAg decreased to levels of 6–77% before the fifth POD and remained low at approximately 80%, influenced by the pumping even after the 25th POD. In summary, VADs themselves activated coagulation and induced consumption coagulopathy to some degree. However, most of the parameters returned to normal within 2 weeks.
"Understanding the Elephant: The Discourse Approach to Boundary Identification and Corpus Construction for Theory Review Articles" (2019)

The goal of a review article is to present the current state of knowledge in a research area. Two important initial steps in writing a review article are boundary identification (identifying a body of potentially relevant past research) and corpus construction (selecting research manuscripts to include in the review). We present a theory-as-discourse approach, which (1) creates a theory ecosystem of potentially relevant prior research using a citation-network approach to boundary identification; and (2) identifies manuscripts for consideration using machine learning or random selection. We demonstrate an instantiation of the theory as discourse approach through a proof-of-concept, which we call the automated detection of implicit theory (ADIT) technique. ADIT improves performance over the conventional approach as practiced in past technology acceptance model reviews (i.e., keyword search, sometimes manual citation chaining); it identifies a set of research manuscripts that is more comprehensive and at least as precise. Our analysis shows that the conventional approach failed to identify a majority of past research. Like the three blind men examining the elephant, the conventional approach distorts the totality of the phenomenon. ADIT also enables researchers to statistically estimate the number of relevant manuscripts that were excluded from the resulting review article, thus enabling an assessment of the review article’s representativeness.
Online tomato inspection using x-ray radiographies and 3-dimensional shape models (2015)

A method is proposed that fits a 3-dimensional shape model (SM) on X-ray radiographies of tomatoes on a conveyor belt to allow for inspection of internal tomato quality using X-ray. For the training of the SM a set of computed tomography (CT) scans is used. From these scans, the surfaces of the fruits are extracted. Corresponding points on all these surfaces are located after which the variation in position of every point can be determined using Principal component analysis (PCA). The result of this process is a mean shape with various modes of variation, which represent the variability of the shape. Any shape can then be reconstructed through a linear combination of the mean shape and its modes of variation. During runtime, the contour of every tomato is extracted onto which the SM is fitted. This allows us to accurately estimate tomato volume and 3-dimensional shape, and assess the presence of defects and other unwanted properties from X-ray radiographies in an online application. Results are promising, but show that improvement can be made by simulating radiographs from the shape model and fitting these directly to the easured radiograph.
Supplementary table 2 from Dose–Response Relationship in Phase I Clinical Trials: A European Drug Development Network (EDDN) Collaboration Study (2023)

&lt;p&gt;Supplementary table 2. Multivariate model for overall survival (Molecularly Targeted Agents).&lt;/p&gt;
Spontaneous and iatrogenic spreading of liver-derived cells into peripheral blood of patients with primary liver cancer (1997)

The prognosis for patients with primary liver cancer (PLC) often depends on tumor recurrence and the development of extrahepatic metastases, particularly after liver transplantation. We have developed a sensitive test to detect both spontaneous circulation of tumor cells and the spread of liver cells due to chemoembolization and alcoholization. Reverse-transcription polymerase chain reaction was used to search for cells expressing alpha-fetoprotein (AFP) messenger RNA in the peripheral blood of 84 patients with PLC and 102 controls (55 patients with chronic hepatitis and/or cirrhosis, 10 patients with benign liver tumors or liver metastases from intestinal cancers, and 37 healthy individuals). By spiking the blood of healthy volunteers with HepG2 cells, we assessed the sensitivity limit: one HepG2 cell mixed with 10(7) leukocytes. All 102 controls tested negative. In contrast, 28 patients (33.3%) with PLC tested positive. Positivity for the test was significantly associated with portal thrombosis, tumor size, intravascular tumor emboli, serum AFP level, and extrahepatic metastases. Patients were followed up for a mean period of 39 +/- 51 weeks: the probability of developing extrahepatic metastases was significantly higher in positive than in negative patients. Eighteen negative patients with PLC were tested before, 1 hour after, and 24 hours after locoregional therapy: 9 tested positive either 1 or 24 hours after alcoholization or chemoembolization. In conclusion, we have developed a highly specific and sensitive test to detect circulating tumor cells in patients with PLC. This test is likely to be clinically useful in evaluating the risk of developing extrahepatic metastases and the possibility of iatrogenic spreading of liver-derived, possibly tumorous, cells.
Tracking of Metallic Objects Using a Retro-Reflective Array at 26 GHz (2010)

The detection and tracking of targets in highly cluttered environments often poses a difficult engineering challenge as the strong clutter backscatter contained in the scene makes it difficult to distinguish the target of interest. A design concept to aide in standoff detection and tracking of large metallic objects in a warehouse setting is presented. This includes the design and implementation of an active retro-reflective array system that is able to determine the precise location and identification of an object. To accomplish this, a unique series fed grounded coplanar waveguide patch antenna is designed and implemented with minimal cross coupling among elements. This compact array has a relatively large radar cross-section (RCS) while maintaining the desired retro-reflectivity. Additionally, a tilted beam is incorporated in the linear series-fed array to isolate the large RCS of the planar array structure at boresight from the desired modulated, retro-reflective RCS. This method for enhanced detection is implemented at 26 GHz. The incorporation of the high-speed PIN switches into the array structure provide the tag with a unique identification. Measurement results for the modulated RCS from such an array in a cluttered environment are presented.
Actin binding proteins in blood–testis barrier function (2015)

We provide a model on how ABPs regulate BTB remodeling, shedding new light on unexplained male infertility, such as environmental toxicant-induced reproductive dysfunction since the testis, in particular the BTB, is sensitive to environmental toxicants, such as cadmium, bisphenol A, phthalates, and PFOS (perfluorooctanesulfonic acid or perfluorooctane sulfonate).
Reliability testing and test structure design in an age of increasing variability (2013)

Two challenges of semiconductor device scaling are: 1) process complexity increases with each generation 2) variability increases with device scaling. The impact of 1) is clear to anyone involved in early process development, when apparently trivial changes in process for high-kmetal gate stacks can lead to significant changes in such reliability characteristics as BTI time slope, magnitude, and recovery, all often treated as universals in reliability literature. Almost by definition 2) could be considered most challenging in reliability relative to other areas of semiconductor engineering because in practice semiconductor reliability is the study of spatially and temporally rare events often involving one or several atoms. The two challenges are intimately linked because when advanced process node features such as stress liners, stress memorization and raised source/drains play a role in device performance, the channellength/width become only one piece of the layout induced variability. These challenges drive the need for faster reliability measurements done in higher volume. Testing can be done on individual devices with several SMUs, through simplified decoder structures with thousands of devices, to full product level using very expensive APGs. We discuss some of the engineering and (necessarily) economic choices that drive the techniques and structures used for electrical measurements made at each of these levels.
Time course of vasospasm in man (1978)

Measurements were made at eight predetermined positions on 627 sets of angiograms from 293 patients with aneurysms. A ratio between the sum of the vessel diameters in the subarachnoid space to the sum in the base of skull and neck was calculated and plotted against time. Vasospasm has its onset in man about Day 3 after subarachnoid hemorrhage, is maximal at Days 6 to 8, and is gone by Day 12. There is a tendency for patients in poor clinical grades to have more vasospasm. The patients with most vasospasm have a significantly higher mortality than those with the least.
Approximation Algorithm for Process Mapping on Network Processor Architectures (2007)

The high performance requirements of networking applications has led to the advent of programmable network processor (NP) architectures that incorporate symmetric multiprocessing, and block multi-threading. The paper presents an automated system-level design technique for process mapping on such architectures with an objective of maximizing the worst case throughput of the application. As this mapping must be done in the presence of resource (processors and code size) constraints, this is an NP-complete problem (Ausiello et al., 1999). We present a polynomial time approximation algorithm guaranteed to generate solutions with throughput at least 1/2 that of optimal solutions. The proposed algorithm was utilized to map realistic applications on the Intel IXP2400 (NP) architecture, and produced solutions within 78% of optimal.
Alveolar Macrophage ABCG1 Deficiency Promotes Pulmonary Granulomatous Inflammation (2019)

Pulmonary granuloma formation is a complex and poorly understood response to inhaled pathogens and particulate matter. To explore the mechanisms of pulmonary granuloma formation and maintenance, our laboratory has developed a multiwall carbon nanotube (MWCNT)-induced murine model of chronic granulomatous inflammation. We have demonstrated that the MWCNT model closely mimics pulmonary sarcoidosis pathophysiology, including the deficiency of alveolar macrophage ATP-binding cassette (ABC) lipid transporters ABCA1 and ABCG1. We hypothesized that deficiency of alveolar macrophage ABCA1 and ABCG1 would promote pulmonary granuloma formation and inflammation. To test this hypothesis, the effects of MWCNT instillation were evaluated in ABCA1, ABCG1, and ABCA1/ABCG1 myeloid-specific knockout (KO) mice. Histological examination revealed significantly larger pulmonary granulomas in ABCG1-KO and ABCA1/ABCG1 double-KO animals when compared with wild-type animals. Evaluation of BAL cells indicated increased expression of CCL2 and osteopontin, genes shown to be involved in the formation and maintenance of pulmonary granulomas. Single deficiency of alveolar macrophage ABCA1 did not affect MWCNT-induced granuloma formation or proinflammatory gene expression. These observations indicate that the deficiency of alveolar macrophage ABCG1 promotes pulmonary granulomatous inflammation and that this is augmented by additional deletion of ABCA1.
Towards Integration of Quadratic Placement and Pin Assignment (2005)

Pins serve as both the logical and physical interface between two levels in a hierarchical flow. Pin assignment is the placement of pins on the boundary of a chip or macro. Proper pin placement has a large influence on wire length. Experiments indicate a spread in wire length up to over 20%. To address the pin assignment problem, a modification to the well-known and widely used quadratic placement is introduced. This modification allows for the integration between pin assignment and global placement. Wire length within macros is minimized, while top-level considerations such as the relative position of macro and clusters of cells are taken into account in the form of a side assignment. As indicated by experimental results, integration is promising. More research is necessary to fully exploit the ideas in this paper, and assess the practical impact of the approach.
Detection of Resistance to Beta-Lactamase Inhibitors in Strains with CTX-M Beta-Lactamases: a Multicenter External Proficiency Study Using a Well-Defined Collection of Escherichia coli Strains (2013)

Under the auspices of the Spanish Society for Infectious Diseases and Clinical Microbiology Quality Control program, 14 Escherichia coli strains masked as blood culture isolates were sent to 68 clinical microbiology laboratories for antimicrobial susceptibility testing to β-lactam antibiotics. This collection included three control strains (E. coli ATCC 25922, an IRT-2 producer, and a CMY-2 producer), six isogenic strains with or without the OmpF porin and expressing CTX-M β-lactamases (CTX-M-1, CTX-M-15, and CTX-M-14), one strain carrying a double mechanism for β-lactam resistance (i.e., carrying CTX-M-15 and OXA-1 enzymes), and four strains carrying CTX-M variants with different levels of resistance to β-lactams and β-lactam-β-lactamase inhibitor (BLBLI) combinations. The main objective of the study was to ascertain how these variants with reduced susceptibilities to BLBLIs are identified in clinical microbiology laboratories. CTX-M variants with high resistance to BLBLIs were mainly identified as inhibitor-resistant TEM (IRT) enzymes (68.0%); however, isogenic CTX-M mutant strains with reduced susceptibilities to BLBLIs and cephalosporins were mainly associated with extended-spectrum β-lactamase production alone (51 to 80%) or in combination with other mechanisms (14 to 31%). Concerning all β-lactams tested, the overall interpretative discrepancy rate was 11.5%, of which 38.1% were the consequence of postreading changes in the clinical categories when a resistance mechanism was inferred. Therefore, failure to recognize these complex phenotypes might contribute to an explanation of their apparent absence in the clinical setting and might lead to inadequate drug treatment selection. A proposal for improving recognition is to adhere strictly to the current CLSI or EUCAST guidelines for detecting reduced susceptibility to BLBLI combinations, without any interpretative modification.
Panoramic Robust PCA for Foreground-Background Separation on Noisy,\n Free-Motion Camera Video (2017)

This work presents a new robust PCA method for foreground-background\nseparation on freely moving camera video with possible dense and sparse\ncorruptions. Our proposed method registers the frames of the corrupted video\nand then encodes the varying perspective arising from camera motion as missing\ndata in a global model. This formulation allows our algorithm to produce a\npanoramic background component that automatically stitches together corrupted\ndata from partially overlapping frames to reconstruct the full field of view.\nWe model the registered video as the sum of a low-rank component that captures\nthe background, a smooth component that captures the dynamic foreground of the\nscene, and a sparse component that isolates possible outliers and other sparse\ncorruptions in the video. The low-rank portion of our model is based on a\nrecent low-rank matrix estimator (OptShrink) that has been shown to yield\nsuperior low-rank subspace estimates in practice. To estimate the smooth\nforeground component of our model, we use a weighted total variation framework\nthat enables our method to reliably decouple the true foreground of the video\nfrom sparse corruptions. We perform extensive numerical experiments on both\nstatic and moving camera video subject to a variety of dense and sparse\ncorruptions. Our experiments demonstrate the state-of-the-art performance of\nour proposed method compared to existing methods both in terms of foreground\nand background estimation accuracy.\n
Utilizing click chemistry to design functional interfaces through post-polymerization modification (2012)

Post-polymerization modification is a simple and effective method to add complex functionality to a polymeric interface. A wide variety of click reactions have been utilized as a means of post-polymerization functionalization on surface-bound polymers to tune interfacial properties, such as friction, wettability, and adhesion. Patterning surfaces with spatial control of chemical functionality has also been obtained through orthogonal or sequential click reactions. This review highlights the progress in post-polymerization modification of polymers covalently attached to a surface, focusing on the design of functional interfaces in terms of the various reactive functional groups.
Subclass and avidity of circumsporozoite protein specific antibodies associate with protection status against malaria infection (2021)

RTS,S/AS01 is an advanced pre-erythrocytic malaria vaccine candidate with demonstrated vaccine efficacy up to 86.7% in controlled human malaria infection (CHMI) studies; however, reproducible immune correlates of protection (CoP) are elusive. To identify candidates of humoral correlates of vaccine mediated protection, we measured antibody magnitude, subclass, and avidity for Plasmodium falciparum (Pf) circumsporozoite protein (CSP) by multiplex assays in two CHMI studies with varying RTS,S/AS01B vaccine dose and timing regimens. Central repeat (NANP6) IgG1 magnitude correlated best with protection status in univariate analyses and was the most predictive for protection in a multivariate model. NANP6 IgG3 magnitude, CSP IgG1 magnitude, and total serum antibody dissociation phase area-under-the-curve for NANP6, CSP, NPNA3, and N-interface binding were also associated with protection status in the regimen adjusted univariate analysis. Identification of multiple immune response features that associate with protection status, such as antibody subclasses, fine specificity and avidity reported here may accelerate development of highly efficacious vaccines against P. falciparum.
On the roles of extracellular matrix remodeling by gelatinase B. (1997)

Human extracellular matrix is constantly remodelled by de novo synthesis of structural components and by degradation of the matrix proteins by various proteinases. The secreted proteolytic enzymes are regulated at several levels: by control of gene transcription, by glycosylation, by specific inhibitors and by enzyme activation processes. The latter level most often involves clipping of a proenzyme or zymogen into an active proteinase. A series of such activation reactions leads to enzyme cascades. Whereas proteolytic activation is an all-or-none phenomenon, glycosylation usually has a restricted or fine-tuning effect on the catalytic activity of enzymes. Commonly, a two- to threefold reduction in specific activity is imposed by N-glycosylation on each member of the multi-enzyme chain. In a series comprising e.g. four enzymes, this can lead to significant influences (2(4)-3(4)-fold increase) on the substrate converting activity of the terminal member of a cascade. Gelatinase B is a terminal member of the protease cascade which leads to matrix degradation. It cleaves gelatins (denatured collagens or collagen fragments after digestion by collagenase) and other substrates and is thought to be involved in matrix remodeling during the normal processes of embryogenesis, tissue remodeling and development. Gelatinase B expression is upregulated in pathological states such as invasion of cancer cells and when leukocytes are released from the bone marrow and migrate towards an inflammatory focus. Proteases, including gelatinase B, are transcriptionally regulated by cytokines and directly by the activation processes. The gene regulation of enzyme inhibitors as well as other humoral factors, which contribute to protease activation, influence protease activities in an indirect way. Proteases might also play a role in the pathophysiology of chronic inflammation and autoimmunity by cleaving extracellular structural proteins and by generating proteolytic fragments. Indeed, these remnant fragments antigenically resemble the original precursor proteins, but are structurally and quantitatively different and may provoke an autoimmune response. Application of the knowledge of the structure, function and regulation of gelatinase B has contributed to the understanding of the mechanism of action of some gelatinase-inhibiting antirheumatic drugs and promises to contribute further to the development of novel treatment strategies for autoimmune diseases such as multiple sclerosis and for invasive cancers.