cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
QCD ghost reconstruction of f(T) gravity in flat FRW universe
Creators: name: Chattopadhyay, Surajit
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The present work reports a reconstruction scheme for f(T) gravity based on QCD ghost dark energy. Two models of f(T) have been generated and the pressure and density contributions due to torsion have been reconstructed. Two realistic models have been obtained and the effective equations of state have been studied. Also, the squared speed of sound has been studied to examine the stability of the models.
description: 13 pages, 8 figures, Accepted for publication in European Physical Journal Plus
A Low-cost Strategic Monitoring Approach for Scalable and Interpretable Error Detection in Deep Neural Networks
Creators: name: Geissler, Florian
name: Qutub, Syed
name: Paulitsch, Michael
name: Pattabiraman, Karthik
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: We present a highly compact run-time monitoring approach for deep computer vision networks that extracts selected knowledge from only a few (down to merely two) hidden layers, yet can efficiently detect silent data corruption originating from both hardware memory and input faults. Building on the insight that critical faults typically manifest as peak or bulk shifts in the activation distribution of the affected network layers, we use strategically placed quantile markers to make accurate estimates about the anomaly of the current inference as a whole. Importantly, the detector component itself is kept algorithmically transparent to render the categorization of regular and abnormal behavior interpretable to a human. Our technique achieves up to ~96% precision and ~98% recall of detection. Compared to state-of-the-art anomaly detection techniques, this approach requires minimal compute overhead (as little as 0.3% with respect to non-supervised inference time) and contributes to the explainability of the model.
title: Global Prevention of Adult Cancers
Creators: name: Raso, Vic
Publisher: name: eScholarship@UMMS
Year: 2013

description: Growth hormone receptor deficient (GHRD) individuals in Ecuador are cancer free their entire lifetime due to low insulin-like growth factor (IGF) levels. This IGF deficiency protected that small GHRD population from the wide array of 20 different cancer types that caused death in their IGF-replete relatives. This suggests that the initiation or progression of many human cancers is dependent on IGF.

Those GHRD individuals are short statured due to their life-long IGF deficit but otherwise are surprisingly healthy and long-lived (some >80 years old). Therefore, we are developing IGF-suppressive vaccines for use in fully grown adults with the hope of gaining the same potent anti-cancer impact seen in low IGF individuals with GHRD.

This compelling human example of the cancer prevention benefits of low IGF activity coupled with its probable safety in physically mature people form the basis of our unprecedented cancer suppression strategy. We designed specific vaccines to prevent the emergence of age-dependent cancers by cutting off their essential early supply of IGF.

Our vaccines actively induce antibodies to neutralize IGF directly or obstruct the activity of a key enzyme that regulates IGF bioavailability. Protective vaccination would be initiated at middle age since most human cancers occur beyond age 60 and since this postponement will circumvent any impairment of normal growth or other functions. The continuous presence of those inhibitory antibodies will keep IGF activity at a constantly low level and thereby preemptively block the development of incipient cancers later in life.

These prevention vaccines could be used: 1) for people with a genetically high likelihood for developing familial forms of cancer, 2) as an adjuvant therapy following precancerous growth removal, 3) to inhibit the recurrence of disease for cancer patients who are in remission, and 4) as a general prophylactic to protect against spontaneous, age-dependent cancers.
Additional file 7 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
Creators: name: Henkel, Luisa
name: Rauscher, Benedikt
name: Schmitt, Barbara
name: Winter, Jan
name: Boutros, Michael
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 7: Figure S3. DNA content analysis to determine ploidy of various HAP1 Cas9 populations. (A) HAP1 Cas9 bulk and HAP1 Cas9 SCC11 and SCC12 cells were stained for DNA content using Nicoletti buffer and FACS analysis. The percentage of G1 haploid cells and G2 diploid cells are indicated for each cell population (n = 2 for each condition). (B-C) Enriched haploid and diploid populations of the HAP1 Cas9 SCC11 (B) and Cas9 SCC12 (C) cell lines were obtained by FACS sorting. Subsequently, haploid and diploid populations were independently transduced with the HDCRISPRv1 vector expressing sgRNAs targeting the surface marker CD46 and editing efficiency was directly compared in the haploid and diploid population of the same cell line. Non-edited samples of the respective cell lines served as a control. Lines represent the mean of three independent experiments for each condition.
Collaboration with Conversational AI Assistants for UX Evaluation: Questions and How to Ask them (Voice vs. Text)
Creators: name: Kuang, Emily
name: Soure, Ehsan Jahangirzadeh
name: Fan, Mingming
name: Zhao, Jian
name: Shinohara, Kristen
Publisher: name: arXiv
Year: 2023
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: AI is promising in assisting UX evaluators with analyzing usability tests, but its judgments are typically presented as non-interactive visualizations. Evaluators may have questions about test recordings, but have no way of asking them. Interactive conversational assistants provide a Q&A dynamic that may improve analysis efficiency and evaluator autonomy. To understand the full range of analysis-related questions, we conducted a Wizard-of-Oz design probe study with 20 participants who interacted with simulated AI assistants via text or voice. We found that participants asked for five categories of information: user actions, user mental model, help from the AI assistant, product and task information, and user demographics. Those who used the text assistant asked more questions, but the question lengths were similar. The text assistant was perceived as significantly more efficient, but both were rated equally in satisfaction and trust. We also provide design considerations for future conversational AI assistants for UX evaluation.
description: Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI '23), April 23--28, 2023, Hamburg, Germany
title: A Nutritional Formulation for Cognitive Performance and Mood in Alzheimer’s Disease and Mild Cognitive Impairment: A Phase II Multi-site Randomized Trial with an Open-label Extension
Creators: name: Remington, Ruth
name: Bechtel, Cynthia
name: Larsen, David
name: Lortie, Jevin J.
name: Samar, Annemarie
name: Doshanjh, Laura
name: Fishman, Paul
name: Luo, Yuan
name: Smyers, Kathleen
name: Hoffman, Heather
name: Barysauskas, Constance
name: Barton, Bruce A.
name: Shea, Thomas B.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background: It is increasingly recognized that interventions for dementia must shift towards prevention to obtain maximal efficacy and any significant degree of disease modification. Nutritional supplementation with single agents has shown varied results, suggesting the need for combinatorial intervention.

Methods: We conducted a 3-month, randomized, multi-site, phase II study in which 141 individuals diagnosed with Alzheimer’s disease (AD) and 34 individuals with Mild Cognitive Impairment received a nutraceutical formulation (NF; folate, alpha-tocopherol, B12, S-adenosyl methioinine, N-acetyl cysteine, acetyl-L-carnitine) or indistinguishable placebo under double-blind conditions, followed by an open-label extension in which all individuals received NF for a total of 1yr. An additional 38 individuals with AD received NF under open-label conditions from baseline for 1yr. The primary outcome was defined as cognitive performance. Secondary outcomes were defined as behavioral and psychological symptoms of dementia and activities of daily living.

Results: Participants randomized to NF improved statistically within 3 months in cognitive performance as ascertained by Clox-1 and the Dementia Rating Scale, and their caregivers reported improvement in Neuropsychiatric Inventory. Participants receiving NF either continued to improve or maintained their baseline performance during open-label extensions. Participants randomized to placebo did not improve, but during open-label extensions displayed similar improvement within 3 months to that of participants initially randomized to NF. Caregivers reported no change in Activities of Daily Living for either cohort.

Conclusions: These findings confirm and extend prior phase I studies in which NF improved or maintained cognitive performance and behavioral symptoms for individuals with AD, and improved cognitive performance for community-dwelling individuals without dementia. In published studies with transgenic mice NF reduced PS-1 expression, beta and gamma secretase activity, Abeta deposits, phospho-tau, homocysteine and oxidative damage, and increased acetylcholine and glutathione. This comprehensive impact of NF on AD-related neuropathology supports the possibility that NF may harbor disease-modifying properties.
Additional file 5 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
Creators: name: Henkel, Luisa
name: Rauscher, Benedikt
name: Schmitt, Barbara
name: Winter, Jan
name: Boutros, Michael
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5: Figure S2. Features and performance of the HDCRISPRv1 vector. (A) Composition of the lentiviral HD CRISPR sgRNA expression vector. (B) sgRNA cloning efficiency can be addressed upon transfection of the HDCRISPRv1 vector, since residual GFP stuffer in non-digested vector backbone leads to GFP expression (B.l) (n = 2). Complete removal as achieved when cloning single sgRNAs abolishes GFP expression (B.ll) (n = 2), while remaining stuffer in 10% of the plasmid pool still leads to a substantial amount of GFP positive cells (B.lll) (n = 2). Transduction of the non-digested vector still containing the GFP-stuffer does not result in GFP-expressing cells (B.IV) (n = 1). Scale bar = 100 μM (C) FACS analysis of GFP expression upon transfection of the non-digested HDCRISPRv1 vector (l) (n = 2) or the HDCRISPRv1 vector expressing an sgRNA (ll) (n = 3). A mixture of GFP positive and negative cells can be observed upon transfection of a mixture of stuffer and sgRNA-containing vector (lll and IV) (n = 3 for III and n = 2 for IV). (D) Editing efficiency was furthermore assessed upon transduction of HAP1 Cas9 cells with the HDCRISPRv1 vector expressing sgRNAs targeting the surface proteins CD81, followed by FACS staining of residual CD81 protein to address knockout efficiency. Antibody staining of the non-edited cell line was used as a control. Lines represent the mean of three independent experiments for each condition.
Koszul property and Bogomolov's conjecture
Creators: name: Positselski, Leonid
Publisher: name: arXiv
Year: 2014
Subjects: subject: K-Theory and Homology (math.KT)
subject: Number Theory (math.NT)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics

description: This is an enhanced version of the author's 1998 Harvard Ph.D. thesis, as published by IMRN in 2005. We propose an extension of Bogomolov's conjecture about commutator subgroups of Galois groups to arbitrary fields. A somewhat weaker conjecture is then shown to follow, together with the famous Milnor-Bloch-Kato conjecture, from a certain hypothesis about homological properties of the Milnor K-theory algebras.
description: LaTeX 2e, 30 pages; v.2: arguments improved in the appendix, two remarks inserted at the end. Submitted also to K-theory electronic preprint archives at http://www.math.uiuc.edu/K-theory/0730/
title: Greater Co-morbidity Burden is Associated with Greater Pain and Disability at Time of Total Knee Replacement Among African American Patients
Creators: name: Porter, Anthony
name: Harrold, Leslie R.
name: Chen, Lili
name: Allison, Jeroan J.
name: Noble, Philip
name: Ayers, David C.
name: Franklin, Patricia D.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Introduction: The existence of racial disparities in total joint replacement (TJR) care is well established based on Medicare and VA data.1,3 As compared to white patients, African American TJR patients have lower utilization rates, more pain, poorer function at the time of surgery, and higher post-operative complication rates.2,3 We analyzed a national prospective total knee replacement (TKR) cohort to further investigate patterns of medical and musculoskeletal co-morbidities among African American and white TKR patients.

Methods: Descriptive analyses were performed on a national database (FORCE-TJR) of 3,313 TKR patients from 107 orthopedic surgeons. Data collected include patient sociodemographics (age, gender, race, education, insurance, household income, smoking status), modified Charlson co-morbidity scores, and pre-operative and post-operative pain and function scores (SF-36 PCS and MCS, WOMAC, KOOS/HOOS ADL score). To assess the total musculoskeletal pain burden, WOMAC pain scores were recorded for non-operative weight bearing joints as well as Oswestry low back pain scores. Multivariate models are in progress.

Results: Preliminary descriptive analyses demonstrate a higher medical co-morbidity burden in African American TKR patients as compared to whites (COPD, DM, smoking), as well as worse baseline pain (mean WOMAC pain score = 43.46 vs. 52.92, p

Conclusion: Preliminary results demonstrate significant differences in medical and musculoskeletal co-morbidities that correlate with poorer pain and function scores in African American patients at the time of TKR.
Some exact solutions of the semilocal Popov equations
Creators: name: Kim, Chanju
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study the semilocal version of Popov's vortex equations on $S^2$. Though they are not integrable, we construct two families of exact solutions which are expressed in terms of rational functions on $S^2$. One family is a trivial embedding of Liouville-type solutions of the Popov equations obtained by Manton, where the vortex number is an even integer. The other family of solutions are constructed through a field redefinition which relate the semilocal Popov equation to the original Popov equation but with the ratio of radii $\sqrt{3/2}$, which is not integrable. These solutions have vortex number $N=3n-2$ where $n$ is a positive integer, and hence $N=1$ solutions belong to this family. In particular, we show that the $N=1$ solution with reflection symmetry is the well-known $CP^1$ lump configuration with unit size where the scalars lie on $S^3$ with radius $\sqrt{3/2}$. It generates the uniform magnetic field of a Dirac monopole with unit magnetic charge on $S^2$.
description: 13 pages, minor corrections, version published in Phys.Lett. B
title: Type 2 Diabetes-Induced Hematopoietic Stem Cell Oxidant Stress Attenuates the Differentiation, Skews M1/M2 Specification of Monocytes/Macrophages and Delays Wound Healing in db/db Mice
Creators: name: Yan, Jinglian
name: Tie, Guodong
name: Wang, Shouying
name: Messina, Louis M.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Rationale: After recruitment to wounds, monocytes differentiate into macrophages which play a central role in all stages of wound healing. Wound healing is significantly delayed in type 2 diabetics. Although accumulating evidence suggests that delayed wound healing in type 2 diabetics is related to macrophages specification into M1/M2 phenotypes, the mechanism remains unknown.

Objective: This study tested the hypothesis that type 2 diabetes induces hematopoietic stem cells (HSCs) oxidant stress that reduces their differentiation towards monocytes and skews the specification of M1/M2 phenotype, thereby causing delayed wound healing.

Methods and Results: HSCs were sorted from bone marrow of WT and db/db type 2 diabetic mice. DCF staining showed significant oxidant accumulation in HSCs from db/db mice which was reversed by the antioxidant, N-acetylcysteine (NAC). Bone marrow monocyte concentration (FACS analysis of cell surface markers f4/80, cd14 and cd115) was significantly lower in db/db mice than in WT mice. NAC also reversed the reduced differentiation towards monocytes. Wound closure rate was significantly delayed in db/db mice. Macrophages were isolated from wounds and their concentration and M1/M2 phenotype were quantified by flow cytometry. During the inflammatory phase of wound healing, macrophage concentration was decreased and the proportion of M1 macrophages was lower in db/db mice than in WT mice. During new tissue formation phase, macrophage concentration was decreased and the proportion of M2 macrophage was lower, but M1 macrophage was higher in db/db mice than in WT mice. During tissue remodeling phase, macrophage concentration was increased and M1 macrophage remained higher in db/db mice, but no difference was observed in the proportion of M2 macrophages. The reduced differentiation of HSCs towards monocytes and the delayed wound closure phenotype of db/db mice could be transferred to WT mice by transplanting db/db HSCs into lethally irradiated WT mice.

Conclusion: Type 2 diabetes-induced HSC oxidant stress impairs HSC differentiation towards monocytes, skews the M1/M2 specification of macrophages and thereby accounts for the delayed wound healing. Type 2 diabetes-induced HSC oxidant stress may be a heretofore unrecognized critical regulator of dysinflammation in type 2 diabetics.
Additional file 1 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
Creators: name: Henkel, Luisa
name: Rauscher, Benedikt
name: Schmitt, Barbara
name: Winter, Jan
name: Boutros, Michael
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. HD CRISPR library composition. (A) Precision recall curves for differentiating reference core and nonessential genes based on BAGEL Bayes Factors determined for published fitness screens in GenomeCRISPR. Blue curves indicate screens with an area under the curve (AUC) greater than 0.9. Red screens with an AUC of less than 0.9 were excluded for HD CRISPR sgRNA design. (B) Log2 fold change distributions of core essential (red) and nonessential (blue) reference genes for a high quality (left) and a low quality (right) example screen. (C) Library composition of the HD CRISPR sub-libraries A and B. Horizontal bars on the left indicate the number of designs used from different previously published libraries. The panel on the bottom right shows combinations of libraries, that include designs selected for the HD CRISPR library. The bars above this panel quantify the number of selected sgRNAs for each of these combinations. (D) Distribution of exon ranks targeted by the sgRNAs in the HD CRISPR library. (E) Distribution of the predicted off-target counts (see Materials & Methods) for sgRNAs in the HD CRISPR library. (F) Number of sgRNAs, which remained per gene after pre-filtering and were considered for library design. (G) Phenotypic deviation of published sgRNA phenotypes targeting the same gene. For each gene the difference between the GenomeCRISPR effect scores of the sgRNAs with the smallest and the largest effect scores was calculated. This process was repeated for each library using only those sgRNAs included in that library. Guides selected for the HD CRISPR libraries A and B show a narrow phenotypic deviation in published screens from which they were selected.
Additional file 15 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
Creators: name: Henkel, Luisa
name: Rauscher, Benedikt
name: Schmitt, Barbara
name: Winter, Jan
name: Boutros, Michael
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 15: Figure S10. The identified dependency of HAP1 cells on pluripotency genes and the Fanconi anemia pathway is only partially detected in other published screens conducted in HAP1 cells. (A) Essentiality of Yamanaka factors and Fanconi anemia pathway members in individual HD CRISPR HAP1 and previously published TKO HAP1 CRISPR screens. Red boxes indicate that the gene was found essential and gray indicates non-essentiality. White boxes represent genes that are not targeted by the respective library. (B) siRNA knockdown of the FANCL and FANCE expression using four individual siRNAs each in the HAP1 Cas9 bulk and HAP1 Cas9 SCC11 and SCC12 cell lines. A pool of non-targeting siRNAs was used as a control. Surviving cells were stained with crystal violet solution. (C) Same as (B) for FANCG and FANCM expression. Representative images from four independent experiments conducted for each condition are shown. nt ctrl = non targeting control.
title: Use of Novel Microfluidic Devices to Detect Biomarkers in Blood
Creators: name: Orby, Nese
name: Barry, Carol
Publisher: name: eScholarship@UMMS
Year: 2013

description: Blood analysis is highly important in both medical and scientific fields. Traditionally, blood analysis requires a vial of blood and several processing steps resulting in a time consuming and difficult process. The aim of this research is to find a portable and inexpensive device to carry out fast blood cells separation, count and analysis. Previous work show the capability to analyze and separate blood cells using microfluidic devices resulting in less sample volume and shorter analysis time. Most microfluidic devices share similar fabrication process and materials (soft lithography process in polydimethylsiloxane (PDMS)). ELISA (enzyme-linked immunosorbent assay) is the most common method that these devices use. Microfluidic devices have antibodies microarrays and these antibodies will attract/bind to specific viruses or cells enabling the detection of specific diseases.

Sometimes allergies can’t be diagnosed by the common skin prick test and a blood test is needed. The available blood allergy test is more expensive and takes more days to obtain the results than the skin test. Microfluidic devices using ELISA can measure the blood level of immunoglobulin E (IgE). The IgE are antibodies that the body may make in response to certain allergens. Therefore microfluidic devices can be use to make blood allergy tests in a less expensive and time consuming manner than currently allergy blood tests. Psychological disorders such as bipolar disorder, major depression disorder, posttraumatic stress disorder and schizophrenia, are commonly diagnosed by the physician’s judgment based on the patient description of his symptoms. Sometimes it is difficult to get an accurate diagnosis or determine the severity of the patient’s condition based on this. An accurate genetic blood test it can guarantee that the patients are getting the right medication in the proper dosage amounts and that the patients will search the help they need because mental disorders would be viewed the same as any other medical condition. Researchers identified some genes and proteins that are candidate biomarkers for these disorders. However, these are only suggested biomarkers and the selectivity and sensitivity of these need further testing and investigation in order to be able to obtain accurate diagnosis of mental disorders using blood tests.
Shell-model study for $^{204-210}$Tl isotopes and core excitations across the $Z = 82$ and $N = 126$ shell gaps
Creators: name: Bhoy, Bharti
name: Srivastava, Praveen C.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Nuclear Theory (nucl-th)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: In the present work, the $^{204-210}$Tl isotopes have been investigated by performing large-scale shell-model calculations, including configurations allowing both neutron and proton core excitations across the $Z$ = 82 and $N$ = 126 shell gaps. Inspired by the recent high-spin experimental data, the structure of Tl isotopes has been studied for a considerably large model space. The KHHE interaction has been used for $^{204-206}$Tl isotopes, KHH7B interaction for $^{204-210}$Tl isotopes, and additionally KHM3Y interaction has been used for $^{208}$Tl isotope. The core excitation has been performed using the KHH7B and KHM3Y interactions. The level spectra of $^{204-210}$Tl isotopes are comprehensively described and explained by multi-nucleon couplings of single-particle-hole orbitals within the valence space and by core excitations across $^{208}$Pb core. The well-known isomeric states are analyzed in terms of the shell model configurations.
description: 17 pages, 8 figures
Additional file 14 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
Creators: name: Henkel, Luisa
name: Rauscher, Benedikt
name: Schmitt, Barbara
name: Winter, Jan
name: Boutros, Michael
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 14: Figure S9. HD CRISPR Library design strategy does not enrich for sgRNAs with strong phenotypes presumably caused by off-target effects. Bayes Factor analysis of selected HAP1 context-dependent nonessential genes across different screens conducted with various genome-scale CRISPR libraries in cancer cell lines.
Additional file 13 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library
Creators: name: Henkel, Luisa
name: Rauscher, Benedikt
name: Schmitt, Barbara
name: Winter, Jan
name: Boutros, Michael
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 13: Figure S8. Prediction of sgRNA DNA cutting activity based on control phenotypes. (A) Log2 fold change phenotype distributions for sgRNAs targeting nonessential genes (red) as well as targeting (blue) and non-targeting control sgRNAs (green) across different screens conducted with the HD CRISPR library. The screen with the HD CRISPR library A in HAP1 single cell clone SCC12, which was used for subsequent analyses, is highlighted in red. (B) Fit of a Gaussian mixture model with 4 components for screens in SCC12. Components 1 (yellow) and 2 (blue) represent non-targeting and targeting sgRNAs, respectively. Components 3 and 4 capture the phenotypes of sgRNAs with moderate and severe viability phenotypes. (C) Comparison of true fold change distributions of targeting and non-targeting sgRNAs (solid line) to the distributions estimated by the mixture model components (dashed lines) for both HD CRISPR libraries A and B. (D) Number of sgRNAs associated with each phenotype group targeting essential genes according to MAGeCK analysis. For this representation components 3 and 4 are combined in the red group ‘target phenotype’. sgRNAs are stratified based on their design: ‘empirical essential’ sgRNAs target context-specific essential genes and were selected for the HD CRISPR library based on their previous on-target phenotypes. ‘Empirical nonessential’ sgRNAs are part of previously published libraries and target broadly nonessential genes. They were selected based on their lack of outlier phenotypes. De novo sgRNAs were designed using the software cld [34]. (E) Similar plot as D showing sgRNAs of the HD CRISPR library B associated with each phenotype group.
IEEE Engineering Ethics Cases
Publisher: name: Online Ethics Center
Year: 2006

description: The cases reported on here all came to the attention of the IEEE Ethics Committee during the 1990s. Most came in via the ethics hotline, while the initial contacts for others was via communications addressed to authors of ethics columns that appeared in the IEEE Institute. Most of these cases have not been carefully investigated, although we are fairly confident that the essential information is correct. The outcomes of most of the cases are not known-in some cases matters are still in a state of flux. Names and other information that might identify individuals or organizations have been suppressed or fictionalized.
title: Effects of Transitioning From Conventional Methods to Liquid Based Methods on Unsatisfactory Pap Tests: Results from a Multicenter U.S. Study (poster)
Creators: name: Owens, Christopher L.
name: Peterson, Daniel J.
name: Kamineni, Aruna
name: Buist, Diana S. M.
name: Weinmann, Sheila
name: Ross, Tyler R.
name: Williams, Andrew E.
name: Stark, Azadeh
name: Adams, Kenneth F.
name: Field, Terry S.
Publisher: name: eScholarship@UMMS
Year: 2013

description: Background: Pap testing has transitioned from conventional preparations (CP) to liquid based preparations (LBP) due to perceived superiority of LBPs. Many studies conclude LBPs reduce unsatisfactory (UNSAT) tests however some believe the evidence to substantiate this claim is weak. We studied the effect of the transition from CPs to LBPs on the proportion of UNSAT Pap tests (PT) in four health care systems in the United States participating in the NIH-funded SEARCH project.

Methods: Our study cohort consisted of 548,174 women with 1,443,725 total PTs, ages 21-65 years, between 2000 and 2010. We used segmented regression analysis to estimate the effect of adopting LBPs on the proportion of UNSAT PTs after adjusting for age.

Results: Three sites implementing SurePath LBP experienced significant reductions in UNSAT PTs (Site 1 estimated effect: -2.46% [95% CI: -1.47%, -3.45%], Site 2: -1.78% [95% CI: -1.54%, -2.02%], Site 3: -8.25% [95% CI: -7.33%, -9.17%]. The fourth site implementing ThinPrep LBP did not experience a reduction in UNSAT studies. The relative risk of an UNSAT PT in women > 50 increased after the transition to LBPs (SurePath: RR 2.1 [95% CI: 1.9, 2.2] and ThinPrep: RR 1.7 [95% CI: 1.5, 2.0]).

Conclusions: The observed changes in the proportion of UNSAT PTs varied across the participating sites and it was dependent on the type of LBP technology, age of women and the rates prior to the implementation of this technology.
Serendipitous Discovery of a Thin Stellar Stream near the Galactic Bulge in the Pan-STARRS1 3Pi Survey
Creators: name: Bernard, Edouard J.
name: Ferguson, Annette M. N.
name: Schlafly, Edward F.
name: Abbas, Mohamad
name: Bell, Eric F.
name: Deacon, Niall R.
name: Martin, Nicolas F.
name: Rix, Hans-Walter
name: Sesar, Branimir
name: Slater, Colin T.
name: Peñarrubia, Jorge
name: Wyse, Rosemary F. G.
name: Burgett, William S.
name: Chambers, Kenneth C.
name: Draper, Peter W.
name: Hodapp, Klaus W.
name: Kaiser, Nicholas
name: Kudritzki, Rolf-Peter
name: Magnier, Eugene A.
name: Metcalfe, Nigel
name: Morgan, Jeffrey S.
name: Price, Paul A.
name: Tonry, John L.
name: Wainscoat, Richard J.
name: Waters, Christopher
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We report the discovery of a thin stellar stream found in Pan-STARRS1 photometry near the Galactic bulge in the constellation of Ophiuchus. It appears as a coherent structure in the colour-selected stellar density maps produced to search for tidal debris around nearby globular clusters. The stream is exceptionally short and narrow; it is about 2.5° long and 6' wide in projection. The colour-magnitude diagram of this object, which harbours a blue horizontal-branch, is consistent with an old and relatively metal-poor population ([Fe/H]~-1.3) located 9.5 +/- 0.9 kpc away at (l,b) ~ (5°,+32°), and 5.0 +/- 1.0 kpc from the Galactic centre. These properties argue for a globular cluster as progenitor. The finding of such a prominent, nearby stream suggests that many streams could await discovery in the more densely populated regions of our Galaxy.
description: 5 pages, 3 figures. MNRAS, in press
Facies Analysis Of The Reservoir Rocks In The Sylhet Trough, Bangladesh
Creators: name: Joyanta Dutta
Publisher: name: Department of Geology, Chulalongkorn University
Year: 2012
Subjects: Boka Bil, Tidal Flat, Mouth Bar, Shoreface

description: Bulletin of Earth Sciences of Thailand (BEST), 5, 2, 48-57
Simulations of Emerging Magnetic Flux. II: The formation of Unstable Coronal Flux Ropes and the Initiation of CMEs
Creators: name: Leake, J. E.
name: Linton, M. G.
name: Antiochos, S. K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present results from 3D magnetohydrodynamic (MHD) simulations of the emergence of a twisted convection zone flux tube into a pre-existing coronal dipole field. As in previous simulations, following the partial emergence of the sub-surface flux into the corona, a combination of vortical motions and internal magnetic reconnection forms a coronal flux rope. Then, in the simulations presented here, external reconnection between the emerging field and the pre-existing dipole coronal field allows further expansion of the coronal flux rope into the corona. After sufficient expansion, internal reconnection occurs beneath the coronal flux rope axis, and the flux rope erupts up to the top boundary of the simulation domain ($\sim$ 36 Mm above the surface). We find that the presence of a pre-existing field, orientated in a direction to facilitate reconnection with the emerging field, is vital to the fast rise of the coronal flux rope. The simulations shown in this paper are able to self-consistently create many of the surface and coronal signatures used by coronal mass ejection (CME) models. These signatures include: surface shearing and rotational motions; quadrupolar geometry above the surface; central sheared arcades reconnecting with oppositely orientated overlying dipole fields; the formation of coronal flux ropes underlying potential coronal field; and internal reconnection which resembles the classical flare reconnection scenario. This suggests that proposed mechanisms for the initiation of a CME, such as "magnetic breakout", are operating during the emergence of new active regions.
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Creators: name: Lebehot, Benedicte France
Publisher: name: No Publisher Supplied
Year: 2018

description: This dissertation proposes a chronological and historical study of the works, careers, and place within the music and film industry of a group of French film artists, the actor-singers who were a striking presence from the beginning of the "talkies" to the late 1950s. These actor-singers were an important cultural phenomenon in France because they were developing their singing career as well as their cinematographic career at the same time and with the same success rate in both industries, a feat that has not been done again since them. This work aims to reinstate the actor-singers as such and to show how they embodied a unique and long-lasting cultural phenomenon that was sustainable thanks to their relationship between them and their very own audience who first were listeners and then became spectators because they were eager to watch their favorite singers on a big screen. Each actor-singer attracted a distinct audience because, as singers and so as actors, their public was exclusively loyal to them. And because these artists were now part of the cinematographic life, magazines such as Pour Vous, Cinémonde, Ciné-Miroir welcomed them in their pages at the same rank as full-time actors. With this multiple-industry collaboration and the demonstrated dedication from the audience, a sort of artisanal stardom was experimented through the actor-singers and it proved to be quite effective as it lasted almost three decades.The dissertation examines the careers and works of the six most important of these performers, two from each "generation"--actor-singers who began in the cinema in the early talkies, in the later 1930s, and immediately after world war II. These actor-singers are analyzed comparatively, each one contrasted with one or several others, and chronologically, as their star images develop, or fail to do so, over time.  Aside from the films themselves, the primary historical source, used extensively, is fan magazines, such as Pour Vous.  Also employed are popular biographies of the performers.  The novelty of the dissertation lies, in part, in its systematic use of such "popular" materials, which are normally neglected in academic studies of French cinema.
Hyperbolic second order equations with non-regular time dependent coefficients
Creators: name: Garetto, Claudia
name: Ruzhansky, Michael
Publisher: name: arXiv
Year: 2013
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: {Primary 35L10, 35D30, Secondary 46F05

description: In this paper we study weakly hyperbolic second order equations with time dependent irregular coefficients. This means to assume that the coefficients are less regular than Hölder. The characteristic roots are also allowed to have multiplicities. For such equations, we describe the notion of a `very weak solution' adapted to the type of solutions that exist for regular coefficients. The construction is based on considering Friedrichs-type mollifiers of coefficients and corresponding classical solutions, and their quantitative behaviour in the regularising parameter. We show that even for distributional coefficients, the Cauchy problem does have a very weak solution, and that this notion leads to classical or ultradistributional solutions under conditions when such solutions also exist. In concrete applications, the dependence on the regularising parameter can be traced explicitly.
Nanosilver Linings Case and Workshop Materials
Publisher: name: Online Ethics Center
Year: 2016
Subjects: Emerging Technologies
Ethics and Society
Lab and Workplace Safety
Research and Practice
Responsible Innovation
Safety

description: This is a role play workshop designed for ethics education of STEM graduate students.  It primarily emphasizes societal-level macroethics related to decision-making related to commercial application of emerging nanotechnologies, as opposed to microethics or responsible conduct of research (RCR).  However, students will confront dilemmas at the level of individual contact through perspective-taking in acting as one of seven characters in a hypothetical, but realistic, case.
title: Essays in learning and information design.
Creators: name: Cabrera, Carlo Antonio
Publisher: name: London School of Economics and Political Science (LSE)
Year: 2018
Subjects: subject: HB Economic Theory

description: We re-visit three classical models in information economics.
 The first chapter studies the screening problem for a seller who owns a single good, and a buyer whose valuation for the good is their private information. We allow for the seller to acquire information at some cost about the buyer’s value, in addition to her choice over the probability of trade and the transfer. The seller thus chooses a Blackwell experiment for each announcement that the buyer makes in a direct revelation mechanism. More informative experiments are more costly. Under mild conditions, there are always optimal mechanisms where the seller acquires coarse information about the buyer. In particular, it is always optimal for the seller to choose an experiment that consists of no more than four signals. When the buyer has only two possible values, the same holds for experiments that consist of at most three signals.
 The second chapter examines information disclosure in a setting of strategic experimentation. A group of agents continuously and independently choose between a safe arm and risky arms of the same type. When the arms reveal good news, we are able to achieve efficiency in a class of simple information disclosure mechanisms when the agents are initially optimistic enough about their risky arms, but only when there are not too many agents. When the reverse is true, the mechanism must be transparent. Thus, there is a tradeoff between transparency and efficiency. This tradeoff does not exist in the case of bad news.
 In the final chapter, we borrow insights from social learning theory to understand why institutions have persistent effects. We adapt the classical model in a minimal fashion to accommodate a role for institutions, and demonstrate that social learning is one plausible mechanism of persistence.
Revisiting the Impact of Atmospheric Dispersion and Differential Refraction on Widefield Multiobject Spectroscopic Observations. From VLT/VIMOS to Next Generation Instruments
Creators: name: Sánchez-Janssen, Rubén
name: Mieske, Steffen
name: Selman, Fernando
name: Bristow, Paul
name: Hammersley, Peter
name: Hilker, Michael
name: Rejkuba, Marina
name: Wolff, Burkhard
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: (Abridged) Atmospheric dispersion and field differential refraction impose severe constraints on widefield MOS observations. Flux reduction and spectral distortions must be minimised by a careful planning of the observations -- which is especially true for instruments that use slits instead of fibres. This is the case of VIMOS at the VLT, where MOS observations have been restricted, since the start of operations, to a narrow two-hour range from the meridian to minimise slit losses. We revisit in detail the impact of atmospheric effects on the quality of VIMOS-MOS spectra. We model slit losses across the entire VIMOS FOV as a function of target declination. We explore two different slit orientations at the meridian: along the parallactic angle (North-South), and perpendicular to it (East-West). We show that, for fields culminating at zenith distances larger than 20 deg, slit losses are minimised with slits oriented along the parallactic angle at the meridian. The two-hour angle rule holds for these observations using N-S orientations. Conversely, for fields with zenith angles smaller than 20 deg at culmination, losses are minimised with slits oriented perpendicular to the parallactic angle at the meridian. MOS observations can be effectively extended to plus/minus three hours from the meridian in these cases. In general, night-long observations of a single field will benefit from using the E-W orientation. All-sky or service mode observations, however, require a more elaborate planning that depends on the target declination, and the hour angle of the observations. We establish general rules for the alignment of slits in MOS observations that will increase target observability, enhance the efficiency of operations, and speed up the completion of programmes -- a particularly relevant aspect for the forthcoming spectroscopic public surveys with VIMOS.
description: Accepted to A&A. 11 pages, 15 figures. This paper presents the new recommendations for optimal slit alignment in VLT/VIMOS observations
Minimum Cost Design of Water Distribution Systems
Creators: name: Wood, Don J.
name: Charles, C. O.
Publisher: name: Kentucky Water Resources Research Institute, University of Kentucky
Year: 1973

description: Abstract:
The objective of this study was to develop the analytical tools and procedures for minimum cost design of water distribution systems. Both analog and digital means of carrying out pressure and flow calculations were developed. As a result of this effort, digital programs for pressure and flow calculations in water distribution systems were written and have been widely distributed to practicing engineers. One procedure is based on a direct solution of the basic system equations using a linearization scheme and has several advantages over conventional techniques such as the Hardy Cross method. These include avoiding the need to initially balance the network and an assured convergence of the procedure.
Using this tool a procedure was developed for selecting pipe diameter which will result in a minimum cost design within the prescribed constraints. The method of steepest ascent and dynamic programming concepts were used to carry out the optimization. This procedure applies to closed loop' systems without internal pumping. However, this work provides a basis for extending the concepts to more generalized water distribution systems.
Funding information: The work on which this report is based was supported in part by funds provided by the Office of Water Resources Research, United States Department of Interior, as authorized under the Water Resources Research Act of 1964.
Existence, uniqueness and regularity for a class of semilinear stochastic Volterra equations with multiplicative noise
Creators: name: Baeumer, Boris
name: Geissert, Matthias
name: Kovacs, Mihaly
Publisher: name: arXiv
Year: 2014
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: We consider a class of semilinear Volterra type stochastic evolution equation driven by multiplicative Gaussian noise. The memory kernel, not necessarily analytic, is such that the deterministic linear equation exhibits a parabolic character. Under appropriate Lipschitz-type and linear growth assumptions on the nonlinear terms we show that the unique mild solution is mean-$p$ Hölder continuous with values in an appropriate Sobolev space depending on the kernel and the data. In particular, we obtain pathwise space-time (Sobolev-Hölder) regularity of the solution together with a maximal type bound on the spatial Sobolev norm. As one of the main technical tools we establish a smoothing property of the derivative of the deterministic evolution operator family.
title: Assessing Availability of Healthy Options in Food Stores to Guide Community Transformation Grant Activities in Massachusetts
Creators: name: Olendzki, Barbara C.
name: Land, Thomas
name: Kane, Kevin J.
name: Svencer, Susan
name: Chen, Lili
name: Zheng, Hua
name: Patil, Viji
name: Li, Wenjun
Publisher: name: eScholarship@UMMS
Year: 2013

description: INTRODUCTION. Availability of healthy options in food stores is important to preventing obesity. The Mass in Motion Initiative and two Community Transformation Grant (CTG) projects are conducting statewide longitudinal surveys on availability of major healthy and unhealthy food items in foods stores in Massachusetts (MA).

METHODS. The Community Nutrition Environment Evaluation Data System (C-NEEDS) was developed for food environment surveillance. C-NEEDS takes into account seasonal and geographic variations in food supplies, cultural relevance, and USDA dietary recommendations. Between summer 2012 and winter 2013, 567 food stores in 34 municipalities were surveyed and analyzed. Healthy food availability index (HFAI) was calculated for each store. HFAI has a possible range of 0 to 56, with a higher score indicating a greater availability of healthy food items. Community-level variations in HFAI were analyzed in relation to median household income and housing density.

RESULTS. The HFAI scores had good to excellent inter- and intra-rater reliabilities. Store-level HFAI scores had a bimodal distribution, with over 70% of the stores having a score

DISCUSSION. The majority of the surveyed stores were low in healthy food availability, indicating the need of community interventions. Analysis of store- and community-level variations in availability is useful for CTG programs to formulate and prioritize interventions. Future longitudinal surveys of food stores in the intervention and control communities will help evaluate the effectiveness of CTG interventions.