cssi/SciSciGPT-SciSciNet huggingface dataset:
Nonlinearities in protein space limit the utility of informatics in protein biophysics

We examine the utility of informatic-based methods in computational protein biophysics. To do so, we use newly developed metric functions to define completely independent sequence and structure spaces for a large database of proteins. By investigating the relationship between these spaces, we demonstrate quantitatively the limits of knowledge-based correlation between the sequences and structures of proteins. It is shown that there are well-defined, nonlinear regions of protein space in which dissimilar structures map onto similar sequences (the conformational switch), and dissimilar sequences map onto similar structures (remote homology). These nonlinearities are shown to be quite common-almost half the proteins in our database fall into one or the other of these two regions. They are not anomalies, but rather intrinsic properties of structural encoding in amino acid sequences. It follows that extreme care must be exercised in using bioinformatic data as a basis for computational structure prediction. The implications of these results for protein evolution are examined.
Atomic norm denoising with applications to line spectral estimation

The sub-Nyquist estimation of line spectra is a classical problem in signal processing, but currently popular subspace-based techniques have few guarantees in the presence of noise and rely on a priori knowledge about system model order. Motivated by recent work on atomic norms in inverse problems, we propose a new approach to line spectrum estimation that provides theoretical guarantees for the mean-square-error performance in the presence of noise and without advance knowledge of the model order. We propose an abstract theory of denoising with atomic norms which is specialized to provide a convex optimization problem for estimating the frequencies and phases of a mixture of complex exponentials with guaranteed bounds on the mean-squared-error. In general, our proposed optimization problem has no known polynomial time solution, but we provide an efficient algorithm, called DAST, based on the Fast Fourier Transform that achieves nearly the same error rate. We compare DAST with Cadzow's canonical alternating projection algorithm, which performs marginally better under high signal-to-noise ratios when the model order is known exactly, and demonstrate experimentally that DAST outperforms other denoising techniques, including Cadzow's, over a wide range of signal-to-noise ratios.
Ultrasonically modulated X-ray phase contrast imaging

We show that the radiation pressure exerted by a beam of ultrasound can be used for contrast enhancement in high resolution X-ray imaging of tissue. Interfacial features of objects are highlighted as a result of both the displacement introduced by the ultrasound and the inherent sensitivity of X-ray phase contrast imaging to density variations. The potential of the method is demonstrated by imaging various tumor phantoms and tumors from mice. The directionality of the acoustic radiation force and its localization in space permits the imaging of ultrasound-selected tissue volumes. The results suggest that the method may permit the detection of tumors in soft tissue in their early stages of development.
Methods for estimating spatial trends in Steller sea lion pup production using the Kalman filter

Many species exhibit spatially varying trends in population size and status, often driven by differences among factors affecting individual subpopulations. Estimation and differentiation of such trends may be important for management, and a driving force for monitoring programs. The ability to estimate spatial differences in population trend may depend on assumptions regarding connectivity among subpopulations (stock structure or spatial overlap in stressors), information that is often poorly known. Linear state-space models using the Kalman filter were developed, tested, and applied for trend estimation of pup production for the western Alaska stock of Steller sea lions (Eumetopias jubatus), given only count data. Models were able to estimate trends and abundance even when data were missing. Models that assumed spatial correlation in trend among rookeries were more robust to stock structure assumptions when the stock structure was potentially mis-specified. High levels of spatial correlation among rookeries estimated from Steller sea lion pup count data are consistent with large-scale covariance of population trend within the Steller sea lion metapopulation.
Cellular dynamical mechanisms for encoding the time and place of events along spatiotemporal trajectories in episodic memory

Understanding the mechanisms of episodic memory requires linking behavioral data and lesion effects to data on the dynamics of cellular membrane potentials and population interactions within brain regions. Linking behavior to specific membrane channels and neurochemicals has implications for therapeutic applications. Lesions of the hippocampus, entorhinal cortex and subcortical nuclei impair episodic memory function in humans and animals, and unit recording data from these regions in behaving animals indicate episodic memory processes. Intracellular recording in these regions demonstrates specific cellular properties including resonance, membrane potential oscillations and bistable persistent spiking that could underlie the encoding and retrieval of episodic trajectories. A model presented here shows how intrinsic dynamical properties of neurons could mediate the encoding of episodic memories as complex spatiotemporal trajectories. The dynamics of neurons allow encoding and retrieval of unique episodic trajectories in multiple continuous dimensions including temporal intervals, personal location, the spatial coordinates and sensory features of perceived objects and generated actions, and associations between these elements. The model also addresses how cellular dynamics could underlie unit firing data suggesting mechanisms for coding continuous dimensions of space, time, sensation and action.
Learning Graphical Models for Hypothesis Testing

We propose a novel procedure for learning tractable graphical models from data samples. The traditional approach is to learn models that are generically good approximations of the underlying distributions. In contrast, we are interested in learning models for a specific purpose: binary hypothesis testing. The distributions corresponding to the hypotheses are not available, instead we are given two labelled sets of training samples. Our procedure learns two models, one for each hypothesis, which are then used in a likelihood ratio test for classifying a new unlabelled sample. Each model is learnt from both sets of training samples. Numerical simulations show that our procedure has a lower probability of classification error, as compared to a procedure that learns each model using only its own training set. The gain is more significant when the problem size is larger and the number of training samples available is smaller.
Qualitative age interactions (or effect modification) suggest divergent pathways for early-onset and late-onset breast cancers

21036 Background: Notwithstanding some recent declines, breast cancer incidence rates have risen for decades, though not equally for all age groups. We used the National Cancer Institute's SEER pro...
Shape and mechanical resistance

Before proceeding, it is useful to introduce some new concepts of mechanical physics in relation to the resistance of materials.
Pollen Grains in the Guts of Field Collected Tabanids in Louisiana

Pollen grains in the guts of field-collected flies indicate that tabanid flies obtain carbohydrates from a variety of plants in Louisiana. In alluvial areas, oak ( Quercus ) pollen was most frequently observed in gut contents. In salt marsh areas, grass (Gramineae), composite (Compositae), and oak pollen grains were most abundant.
ROOM TEMPERATURE LIGHT INDUCED ELECTRON SPIN RESONANCE IN UNDOPED HYDROGENATED AMORPHOUS SILICON (a-Si:H).

The effects of illumination upon the absorption electron spin resonance spectrum of the dangling bond defect system have been studied in undoped amorphous hydrogenated silicon (a-Si:H). A small shift of the inhomogeneous envelope of the system towards higher g-value is observed at room-temperature. The shift is not accompanied by a significant change in the signal. Results are reported which indicate that this shift is not due to illumination induced heating of the specimen or calibration changes of the spectrometer. The results may be related to previously reported optical bias effects upon transient photocurrent and photoinduced absorption studies.
Color and Reflectance of Human Flesh

A recent investigation of the variation in spectral reflectance and chromaticity of the flesh tones of various individuals is described. Spectrophotometric reflectance measurements were made on the face, arms and hands of several individuals having different complexions and degrees of sun tan. Spectro-radiometric measurements were made of many phases of daylight. The variations in chromaticity of fleshtones due to daylight variations were calculated. The reflectance of the flesh was computed in terms of the response of an exposure meter to determine the exposure constant for reflected-light readings taken on the human face.
Applying an Evidence-Based Framework to the Early Childhood Coaching Literature

Professional development (PD) is a critical pathway for promoting the use of evidence-based intervention practices in early childhood (EC) settings. Coaching has been proposed as a type of PD that ...
Highly Efficient Mouse Genome Editing by CRISPR Ribonucleoprotein Electroporation of Zygotes

The CRISPR/Cas9 system has been employed to efficiently edit the genomes of diverse model organisms. CRISPR-mediated mouse genome editing is typically accomplished by microinjection of Cas9 DNA/RNA and single guide RNA (sgRNA) into zygotes to generate modified animals in one step. However, microinjection is a technically demanding, labor-intensive, and costly procedure with poor embryo viability. Here, we describe a simple and economic electroporation-based strategy to deliver Cas9/sgRNA ribonucleoproteins into mouse zygotes with 100% efficiency for in vivo genome editing. Our methodology, designated as CRISPR RNP Electroporation of Zygotes (CRISPR-EZ), enables highly efficient and high-throughput genome editing in vivo, with a significant improvement in embryo viability compared with microinjection. Using CRISPR-EZ, we generated a variety of editing schemes in mouse embryos, including indel (insertion/deletion) mutations, point mutations, large deletions, and small insertions. In a proof-of-principle experiment, we used CRISPR-EZ to target the tyrosinase (Tyr) gene, achieving 88% bi-allelic editing and 42% homology-directed repair-mediated precise sequence modification in live mice. Taken together, CRISPR-EZ is simple, economic, high throughput, and highly efficient with the potential to replace microinjection for in vivo genome editing in mice and possibly in other mammals.
Positive Psychology Course and Its Relationship to Well-Being, Depression, and Stress:

The purpose of this study was to determine the influence of a positive psychology course on student well-being, depressive symptoms, and stress in a repeated measure, nonequivalent control design. As hypothesized, the positive psychology students reported higher overall happiness, life satisfaction, routes to happiness, and lower depressive symptoms and stress compared to students in the control course. These findings replicate previous research on the benefits of positive psychology courses on well-being and extend previous research by showing that the benefits generalize to other reliable and multidimensional measures of happiness as well as measures of depression and stress. Our results indicate that a positive psychology course may be one way to improve students’ mental health.
Estrogen Receptor Molecular Biology

A greater understanding of the molecular biology of estrogen receptor (ER) will allow the extension of its utility as a target in therapy to an increased number of patients. The treatment of ER-positive breast cancer with antiestrogens involves a very sophisticated decision. Patients are treated with tamoxifen based on the direct measurement of the level of ER expression in the tumor and an indirect assessment of its activity through the measurement of an important target gene, progesterone receptor (PR). An understanding of the mixed agonist-antagonist nature of tamoxifen has led to the development of pure antagonists with clinical potential. Thus, the hormonal therapy of breast cancer can serve as the paradigm for the rational treatment of cancer based on the presence of the specific target of the therapy in the tumor and an understanding at the molecular level of the function of that target.
Reduction of Salmonella and Campylobacter on Chicken Carcasses by Changing Scalding Temperature.

Chickens were processed at three scalding temperatures, 52, 56, or 60°C, and the numbers of Salmonella and Campylobacter attached to the fully processed carcasses in each group were compared. For S...
Discourses of a cancer diagnosis: Narratives of women in academia

This article explores experiences of women faculty members diagnosed with breast cancer and how, in these circumstances, each navigated the responsibilities and requirements associated with a tenure-track role and their experiences in higher education. This qualitative study used online journaling and photovoice to narrate five women’s experiences with a life-threatening diagnosis in a challenging professional role. Using a feminist standpoint theory lens, the research analyzed a gendered experience in higher education while also exploring how women experience their roles from their own standpoint. Findings for this study focus on the ways that participants found agency and supportive spaces as well as how they managed, adjusted, and responded to the responsibilities of the institution while dealing with their cancer diagnosis. Implications suggest the importance of policies and procedures in providing support and assistance for women faculty members dealing with cancer.
Tutorial on Biostatistics: Linear Regression Analysis of Continuous Correlated Eye Data.

ABSTRACTPurpose: To describe and demonstrate appropriate linear regression methods for analyzing correlated continuous eye data.Methods: We describe several approaches to regression analysis involving both eyes, including mixed effects and marginal models under various covariance structures to account for inter-eye correlation. We demonstrate, with SAS statistical software, applications in a study comparing baseline refractive error between one eye with choroidal neovascularization (CNV) and the unaffected fellow eye, and in a study determining factors associated with visual field in the elderly.Results: When refractive error from both eyes were analyzed with standard linear regression without accounting for inter-eye correlation (adjusting for demographic and ocular covariates), the difference between eyes with CNV and fellow eyes was 0.15 diopters (D; 95% confidence interval, CI −0.03 to 0.32D, p = 0.10). Using a mixed effects model or a marginal model, the estimated difference was the same but with nar...
Criteria for Video Engagement in a Biology MOOC

We have designed a Molecular Biology massive open online course (MOOC) for a global audience. Among the learning aids offered are two types of short video segments: lecture videos (delivered unscripted by a professor) and deep dives (fully scripted and animated). While the engaged learners overwhelmingly watched the lecture video segments through to completion, some watched only a portion of each deep dive. As the deep dives take pains to follow evidence-based best practices and are more labor-intensive to make, further study of this difference in viewer retention would inform future course development decisions. Notably, course organization, length of video, lack of on-screen narrator, and identity of narrator show no correlation with this trend. Interestingly, learners who complete lecture videos but not deep dives have slightly higher overall course grades on average. Thus, our model is that learners with a higher degree of knowledge about the subject matter may feel that they do not need to complete the deep dive videos, while they feel the lecture videos are valuable. Future research will test this model.
"No Alcohol, Please. It's a Family Affair!": Building Community Support for a Bluegrass Festival Through Family Friendliness

The luthier, or maker of stringed instruments, Stuart Mossman, one of the organizers of the first Walnut Valley Festival in Winfield, Kansas, spoke to the local Rotary Club about his plans during a meeting in September 1972. The Winfield Courier summarized his presentation: “Those attending will be people who like country and bluegrass music. Many are over fifty years of age and will bring their families along. Mossman pointed out the entire festival will provide good, clean family entertainment.” The message was reinforced after the fact by Winfield Police Chief A.V. “Gus” Froemming, who praised the event in the newspaper, calling it a “very professional” atmosphere. The Courier said “possibly those who may have had qualms about the weekend had confused a bluegrass festival with a rock and roll festival. However, the police chief remarked that ‘this would be a fine place to take the whole family.’” 1
Creation and Capture of Innovation Returns for Intensive Urban Agriculture Systems

Controlled environment agriculture (CEA) allows food plants to be reproducibly grown under conditions of optimal light, temperature, nutrition, and pest control. Space requirements are minimal, and so CEA is ideal for urban areas. Benefits are clear, but the long term economic viability of this new agricultural system is uncertain. We formalize the strategy space for innovation in CEA and discuss the extent to which it is served by investments in public sector agricultural research. We also present a unifying model of the relationship between the organoleptic and other food attributes desired by consumers and the suites of component technologies and business models capable of delivering these attributes via CEA.
As-needed antihypertensive therapy in surgical patients, why and how: challenging a paradigm.

Hypertension is common in hospitalized patients and there are many causes. Some patients have no prior history of hypertension, few symptoms, and no apparent morbidity related to acute rises in blo...
Cisco Systems, Inc. v. Arista Networks, Inc., Brief Amicus Curiae of Copyright Law Professor Pamela Samuelson

The scenes a faire doctrine, which recognizes elements of a work that are stock, rudimentary, or that arise naturally from a particular theme or setting, is a flexible and capacious limitation on copyright protection that can shield defendants from copyright liability. There are at least five senses in which the scenes a faire doctrine may apply in software copyright cases, including when infringement claims are based on the defendant’s reuse of program command terms. First, program command terms can be scenes a faire insofar as they incorporate official industry standard terms. Second, program commands that are common or stock elements likely to be found in software of that kind may be scenes a faire elements. Third, program commands can also be scenes a faire if they logically flow from the functions to be performed. Fourth, program command terms can be scenes a faire if external factors, including market expectations, constrain programmers’ choices of command terms. Fifth, under controlling Ninth Circuit precedents, program commands, like other user interface elements, can, by virtue of longstanding use in an industry, become standards in that industry, and hence scenes a faire elements. At trial, insofar as the jury heard evidence that Cisco’s command-line interface (“CLI”) terms were standards in one or more of these senses, it could reasonably have concluded that so many elements of the claimed compilation of terms were scenes a faire that Arista’s use of those terms did not infringe. Such a finding is especially likely and appropriate given that compilations of program command terms are generally more functional than expressive. In some cases, program command terms, like functional compilations more generally, have been adjudged too functional to be protectable by copyright law. Some functional compilations, though protectable, have enjoyed a very thin scope of protection. The U.S. Court of Appeals for the Federal Circuit should be skeptical of Cisco’s claim that the CLI elements used by Arista are in themselves a protectable work of authorship that Arista infringed, because those commands were subsets of a larger set of command terms and many were scenes a faire elements.
Evaluation of tricuspid annular plane systolic excursion measured by two-dimensional echocardiography in healthy dogs: repeatability, reference intervals, and comparison with M-mode assessment.

Abstract Introduction We sought to determine the feasibility, measurement variability, and within-day repeatability of tricuspid annular plane systolic excursion (TAPSE) measured by two-dimensional echocardiography (2D TAPSE), generate reference intervals for 2D TAPSE, assess agreement and correlation between 2D TAPSE and the conventional TAPSE measured by M-mode echocardiography (MM TAPSE), and to assess the ability of 2D TAPSE to track a drug-induced decrease in right ventricular (RV) function compared with MM TAPSE. Animals Seventy healthy privately owned dogs of varying bodyweight. Methods All dogs underwent a single echocardiogram to quantify RV function by both TAPSE methods. Ten dogs underwent a second echocardiogram 2–3 h after the first to assess within-day repeatability, and 20 different dogs underwent a second echocardiogram 3-h after atenolol (1 mg/kg per os (PO)). Intraobserver and interobserver measurement variabilities were assessed in 12 randomly selected studies using coefficients of variation. Statistical relationships between 2D TAPSE and bodyweight, gender, heart rate, and age were explored. Results 2D TAPSE could be measured in all dogs. Coefficients of variation for repeatability and measurement variability were low (≤12%). Bodyweight-dependent reference intervals for 2D TAPSE were generated using allometric scaling. TAPSE methods were strongly correlated (r = 0.72; p Conclusions Two-dimensional echocardiography TAPSE appears well suited for clinical assessment of RV function. The TAPSE methods should not be used interchangeably.
A case study in attitude determination and control on the cassini mission to saturn

The Cassini spacecraft design was such that the instruments were fixed mounted to the spacecraft body which required rotation of the entire spacecraft to point the instruments in the proper direction in order to take observations. The operations of the Cassini optical remote sensing instruments required a high level of spacecraft-pointing stability to minimize image distortion during an exposure window. This case study provides highlights of the Cassini missions, and overviews of the hardware, software, and aspects of the systems engineering and operations approaches. It focuses on the flight performance of the Cassini spacecraft's pointing stability with respect to mission requirements, sources of spacecraft jitter, and the two spacecraft control modes using the reaction-wheel assembly or the reaction control system composed of eight thrusters. It also summarizes the steps that needed to be taken to manage attitude control performance over a 20-year flight operations period. 1
Loss of fertility in men with varicocele.

Objective To test the hypothesis that men with varicocele who have already fathered children are immune to the detrimental effect of varicocele on their fertility and will continue to be fertile. If this were the case, one would expect a very low incidence of varicocele in currently infertile men who were able to father a child in the past (secondary infertility) compared with men who have never been fertile (primary infertility). Design Survey of men with male factor infertility. Setting Tertiary care university medical center. Patients One thousand ninety-nine infertile men of whom 98 (9%) met our criteria for secondary infertility. Men with prior vasectomy and men whose partners were over age 40 were excluded. Main Outcome Measure Difference in the incidence of varicocele in men with secondary infertility versus primary infertility. Results A varicocele was palpable in 35% (352/1,001) of men with primary infertility and 81% (79/98) of men with secondary infertility. This difference in the incidence of varicocele was highly significant. Men with secondary infertility and varicocele were slightly older (37.9 versus 33.5 years), had a lower mean sperm concentration (30.2 versus 46.1×10 6 /mL), more abnormally shaped sperm (72% versus 40%,), and higher mean serum follicle-stimulating hormone levels (17.6 versus 7.9mIU/mL,) compared with men with primary infertility and varicocele. Conclusions The incidence of varicocele is much higher in male factor secondary infertility compared with primary infertility. These findings suggest that varicocele causes a progressive decline in fertility and that prior fertility in men with varicocele does not predict resistance to varicocele induced impairment of spermatogenesis. Men with a varicocele may benefit from early evaluation and prophylactic varicocelectomy to prevent future infertility.
Factors Associated with Long-Term Quality of Life After Restorative Proctocolectomy with Ileal Pouch Anal Anastomosis

The aim of this study was to analyze factors associated with quality of life (QoL) after ileal pouch anal anastomosis (IPAA). Patients who underwent IPAA (1983–2015) and replied to QoL questionnaire were identified from an IRB-approved prospectively maintained IPAA-database. QoL was assessed using Cleveland Global Quality of Life (CGQL) questionnaire at 1, 3, 5, and 10 years postoperatively. Patient cohort was divided in two groups: overall QoL score ≤ 0.7 (low) and > 0.7 (high). Demographics, perioperative morbidity, and functional results were analyzed. A total of 4059 patients replied to the questionnaire at the most recent follow-up and were included. A total of 2889 (71%) had overall QoL > 0.7 (group 1) and 1170 (29%) patients had overall QoL ≤ 0.7 (group 2). Patients in group 1 had lower rates of early (44.6 vs. 50.4%, p = 0.003) and late (55.7 vs. 64.5%, p 0.7). Patient’s characteristics and minimal perioperative complications impact patient’s QoL following IPAA not only in the short term, but also in the long term.
Survival Disparities by Race and Ethnicity in Early Esophageal Cancer.

Survival outcome disparities among esophageal cancer patients exist, but are not fully understood. We used the Surveillance, Epidemiology, and End Results (SEER)-Medicare linked database to determine whether survival differences among racial/ethnic patient populations persist after adjusting for demographic and clinical characteristics. Our study included T1-3N0M0 adenocarcinoma and squamous cell cancer patients diagnosed between 2003 and 2011. We compared survival among two racial/ethnic patient subgroups using Cox proportional hazards methods, adjusting for age, sex, histology, marital status, socioeconomics, SEER region, comorbidities, T stage, tumor location, diagnosis year, and treatment received. Among 2025 patients, 87.9% were White and 12.1% were Nonwhite. Median survival was 18.7 months for Whites vs 13.8 months for Nonwhites (p = 0.01). In the unadjusted model, Nonwhite patients had higher risk of mortality (HR = 1.29, 95% CI 1.11–1.49, p < 0.0001) when compared to White patients; however, in the Cox regression adjusted model there was no significant difference (HR = 0.94, 95% CI 0.80–1.10, p = 0.44). Surgery, chemotherapy, younger age, lower T stage, and lower Charlson comorbidity score were significant predictors in the full adjusted model. Differences in mortality risk by race/ethnicity appear to be largely explained by additional factors. In particular, associations were seen in surgery and T stage. Further research is needed to understand potential mechanisms underlying the differences and to better target patients who can benefit from treatment options.
Racial/Ethnic Differences in Influenza and Pneumococcal Vaccination Rates Among Older Adults in New York City and Los Angeles and Orange Counties.

Introduction Disparities in vaccination rates exist among racial/ethnic minority adults. This study examined factors associated with influenza (flu) and pneumococcal vaccination rates among non-Hispanic black, Hispanic, and Asian American adults aged 50 or older living in New York City or Los Angeles and Orange counties in California. Methods We used data collected by the REACH US Risk Factor Survey 2009-2012 in New York City and California. We analyzed data on 14,139 adults aged 50 or older who were categorized as non-Hispanic black (New York City [n = 1,715], California [n = 530]), Hispanic (New York City [n = 2,667], California [n = 1,099]), Chinese American (New York City [n = 1,656]), Korean American (New York City [n = 310]), Filipino American (California [n = 1,515]), or Vietnamese American (California [n = 3,435]). Bivariate analyses examined difference across race/ethnicity and location, and multivariable logistic regression models, adjusting for sociodemographic and health variables, examined flu and pneumococcal vaccination rates. Results Among adults aged 50 or older, the flu vaccination rate was lower among non-Hispanic black respondents (New York City, 53.3%; California, 40.5%) than among Hispanic (New York City, 61.0%; California, 49.4%), Chinese (New York City, 67.6%), Korean (New York City, 60.5%), Filipino (California, 66.2%), and Vietnamese (California, 68.0%) respondents. Among adults aged 65 or older, pneumococcal vaccination rates were lowest among Chinese and Korean respondents in New York City (51.7% and 49.1%, respectively), compared with non-Hispanic black (New York City, 62.0%, California, 65.6%), Hispanic (New York City, 60.0%; California 62.7%), Filipino (California, 63.4%), and Vietnamese (California, 63.8%) respondents. Older age, having had a checkup in the past year, and diabetes diagnosis were significantly associated with flu and pneumococcal vaccination in both locations. Additional variables were significant for some vaccinations and locations. Conclusion When compared with Asian American respondents, non-Hispanic black respondents were least likely to receive the flu vaccine in New York City and California. We found no racial/ethnic differences in pneumococcal vaccination rates. Our findings highlight the need for targeted efforts to increase vaccination rates among racial/ethnic minority older adults.
A simple and effective sampler to collect undisturbed cores from tidal marshes

Core sampling is a common procedure in wetland ecology. A simple and inexpensive sampler is described for field use. Its main advantages are: 1) extraction of undisturbed cores; 7.6 cm diameter and up to 100 cm depth, 2) it is lightweight, sturdy and reliable, 3) it is made from widely available PVC items and 4) it requires minimal skills to assemble. The sampler is introduced in the wetland soil, by rotation, to the desired depth; the tooth-like edge can cut and penetrate through the dense root systems. The sampler is capped with an industrial-type stopper, and pulled up. The core is held in the sampler by suction-negative pressure. A plunger is then used to slowly remove the soil-core and sub-samples are collected. Alternatively, both ends of sampler could be sealed and taken to the lab. An 8 cm long sub-sample was adequate for soil physical, biogeochemical and molecular analysis. The sampler has been tested for 2 years with more than 200 cores taken from tidal wetlands in Chesapeake Bay, Virginia, USA. A negative correlation between salinity and organic matter content at 3-5 and 8-10 cm was found. For the deeper samples (48-50 cm), a positive correlation between salinity and organic matter was observed. The sampler worked satisfactory and it required no maintenance besides cleaning.
The Biobehavioral Legacy of Early Attachment Relationships for Adult Emotional and Interpersonal Functioning

The attachment theory provides a coherent framework for understanding how individuals’ earliest ties to their caregivers during infancy and childhood influence the quality of their adult romantic bonds. Historically, these linkages have been understood chiefly in terms of individuals’ internalized, psychological models of relationships. Yet, we now know that early attachment experiences shape not only individuals’ cognitions and emotions, but also a range of basic physiological systems involved in stress reactivity and regulation, which influence the development and maintenance of adult attachment bonds. The purpose of this chapter is to review this basic model. Specifically, (1) the quality of early caregiving, in interaction with genetically based temperament and overall stress exposure, calibrates the infant’s basic stress-regulatory systems; (2) the infant’s resulting stress-regulatory profile shapes his/her developing capacity for emotion-regulation and his/her emerging interpersonal skills; (3) by adulthood, this variability in interpersonal and stress-regulatory skills affects the formation and maintenance of adult attachment bonds. Importantly, this is not a biologically determinist model, but rather a differential susceptibilities approach in which children with high physiological reactivity to stress may be disproportionately likely to suffer from poor environments but also disproportionately likely to benefit from highly nurturant environments. Directions for future research on such possibilities are outlined.
Emotion dysregulation and posttraumatic stress disorder: a test of the incremental role of difficulties regulating positive emotions.

Background and Objectives: Literature provides support for the role of emotion dysregulation in the development and course of posttraumatic stress disorder (PTSD) among women victims of intimate pa...
A handheld confocal microscope with MEMS-based flat-field scanning for fluorescence-guided surgery

We developed a handheld line-scanned dual-axis confocal microscope for real-time optical biopsy. The device utilizes a novel MEMS-based scanning mechanism for field-flattening, and provides high-speed (16 Hz) fluorescence imaging with sub-nuclear resolution in tissue.
Optical Properties of Layered Hybrid Organic-Inorganic Halide Perovskites: A Tight-Binding GW-BSE Study.

We present a many-body calculation of the band structure and optical spectrum of the layered hybrid organic-inorganic halide perovskites in the Ruddlesden-Popper phase with the general formula A2'An-1MnX3n+1, where n controls the thickness of the primarily inorganic perovskite layers. We calculate the mean-field band structure with spin-orbit coupling, quasi-particle corrections within the GW approximation, and optical spectra using the Bethe-Salpeter equation. The model is parametrized by first-principles calculations and classical electrostatic screening, enabling an accurate but cost-effective study of large unit cells and corresponding n-dependent properties. A transition of the electronic and optical properties from quasi-two-dimensional behavior to three-dimensional behavior is shown for increasing n, and the nonhydrogenic character of the excitonic Rydberg series is analyzed. For methylammonium lead iodide perovskites with butylammonium spacers, our n-dependent 1s and 2s exciton energy levels are in good agreement with those from recently reported experiments, and the 1s exciton binding energy is calculated to be 302 meV for n = 1, 97 meV for n = 5, and 37 meV for n = ∞ (bulk MAPbI3). A calculation for an exfoliated n = 1 bilayer predicts a very large 1s exciton binding energy of 444 meV.
Delta Time Scales Iyengar Inequalities

Here we give the necessary background on delta time scales approach. Then we present general related time scales delta Iyengar type inequalities for all basic norms. We finish with applications to specific time scales like \( \mathbb {R},\) \(\mathbb {Z}\) and \(q^{\overline{\mathbb {Z}}}\), \(q>1.\) See also [5].
Do High Ability Managers Mitigate Litigation Related to Financial Reporting

We provide empirical evidence that incremental to the commonly used industry-based proxy for litigation risk and firm-level attributes, managerial ability in transforming corporate resources into r...
Ecological dynamics of the almond floral microbiome in relation to crop management and pollination

1. Crop tissues harbor microbiomes that can affect host health and yield. However, processes driving microbiome assembly, and resulting effects on ecosystem services, remain poorly understood. This is particularly true of flowering crops that rely on pollinators for yield. 2. We assessed effects of orchard management tactics and landscape context on the flower microbiome in almond, Prunus dulcis. Fourteen orchards (5 conventional, 4 organic, 5 habitat augmentation) were sampled at two bloom stages to characterize bacterial and fungal communities associated with floral tissues. The surveys were complemented by in vitro experiments to assess effects of arrival order and fungicides on nectar microbial communities, and effects of fungicides and microbes on honey bee foraging. Finally, a field trial was conducted to test effects of fungicides and microbes on pollination. 3. As bloom progressed, bacterial and fungal abundance and diversity increased, across all floral tissue types and management strategies. The magnitude by which microbial abundance and diversity were affected varied, with host proximity to apiaries and orchard management having notable effects on bacteria and fungi, respectively. 4. Experiments showed immigration history and fungicides affected the composition of nectar microbial communities, but only fungicides affected pollinator foraging through reduced nectar removal. Neither treatment affected pollination services. 5. Synthesis and applications. Our results shed light on routes through which management practices can shape microbiota associated with flowers of a pollinator-dependent crop. With growing appreciation for the role of floral-associated microbes in affecting biotic interactions at the floral interface, understanding such drivers can potentially inform microbial-derived ecosystem services in agricultural landscapes, including pollination and biocontrol.
Risk of bone fractures after the diagnosis of adrenal adenomas: a population-based cohort study.

Objective Several small studies reported increased prevalence and incidence of asymptomatic vertebral fractures in patients with non-functioning adrenal adenomas and adenomas with mild autonomous cortisol secretion. However, the risk of symptomatic fractures at vertebrae, and at other sites remains unknown. Our objective was to determine the prevalence and incidence of symptomatic site-specific fractures in patients with adrenal adenomas. Design Population-based cohort study, Olmsted County, Minnesota, USA, 1995-2017. Methods Participants were the patients with adrenal adenoma and age/sex-matched referent subjects. Patients with overt hormone excess were excluded. Main outcomes measures were prevalence and incidence of bone fractures. Results Of 1004 patients with adrenal adenomas, 582 (58%) were women, and median age at diagnosis was 63 years (20-96). At the time of diagnosis, patients had a higher prevalence of previous fractures than referent subjects (any fracture: 47.9% vs 41.3%, P = 0.003, vertebral fracture: 6.4% vs 3.6%, P = 0.004, combined osteoporotic sites: 16.6% vs 13.3%, P = 0.04). Median duration of follow-up was 6.8 years (range: 0-21.9 years). After adjusting for age, sex, BMI, tobacco use, prior history of fracture, and common causes of secondary osteoporosis, patients with adenoma had hazard ratio of 1.27 (95% CI: 1.07-1.52) for developing a new fracture during follow up when compared to referent subjects. Conclusions Patients with adrenal adenomas have higher prevalence of fractures at the time of diagnosis and increased risk to develop new fractures when compared to referent subjects.
Advanced Retinal Imaging and Ocular Parameters of the Rhesus Macaque Eye

Author(s): Lin, Kira H; Tran, Tu; Kim, Soohyun; Park, Sangwan; Stout, J Timothy; Chen, Rui; Rogers, Jeffrey; Yiu, Glenn; Thomasy, Sara; Moshiri, Ala | Abstract: PurposeTo determine the range of normal ocular biometry and perform advanced retinal imaging and functional assessment of the rhesus macaque eye.MethodsWe performed ocular phenotyping on rhesus macaques at the California National Primate Research Center. This process consisted of anterior and posterior segment eye examination by ophthalmologists, advanced retinal imaging, and functional retinal electrophysiology.ResultsFull eye examinations were performed on 142 animals, consisting of pupillary light reflex, tonometry, external examination and photography, anterior slit lamp examination, and posterior segment examination by indirect ophthalmoscopy. Ages of the rhesus macaques ranged from 0.7 to 29 years (mean, 16.4 ± 7.5 years). Anterior segment measurements such as intraocular pressure (n = 142), corneal thickness (n = 84), lens thickness (n = 114), and axial length (n = 114) were acquired. Advanced retinal imaging in the form of fundus photography (n = 78), optical coherence tomography (n = 60), and quantitative autofluorescence (n = 44) was obtained. Electroretinography (n = 75) was used to assay retinal function. Quantitative analyses of the macular structure, retinal layer segmentation, and rod and cone photoreceptor electrical responses are reported. Quantitative assessments were made and variations between sexes were analyzed to compare with established sex changes in human eyes.ConclusionsThe rhesus macaque has an ocular structure and function very similar to that of the human eye. In particular macular structure and retinal function is very similar to humans, making this species particularly useful for the study of macular biology and development of therapies for cone photoreceptor disorders.Translational relevanceRhesus macaques are an ideal model for future vision science studies of human eye diseases.
Prognostic value of FDG-PET in lymphoma patients undergoing autologous stem cell transplantation

1673 Objectives: High-dose chemotherapy followed by autologous stem cell transplantation (ASCT) is a standard treatment for patients (pts) with relapsed or primary refractory lymphoma that is responding to salvage chemotherapy. Limitations of ASCT include significant morbidity, cost, restriction of further treatment options, and frequent relapse of lymphoma. Methods: . To define the ability of FDG-PET to predict clinical outcome after ASCT, we conducted a retrospective analysis of lymphoma pts in our institution who received salvage chemotherapy followed by ASCT for relapsed or primary refractory lymphoma between 1999 and 2005. We identified 50 lymphoma pts (20 with diffuse large B-cell, 19 with Hodgkin, 5 with mantle cell, 3 with follicular and 3 with other lymphomas) who had an FDG-PET scan after at least two cycles of salvage chemotherapy and prior to ASCT. One pt was excluded from the analysis because the FDG-PET scan result was non-conclusive. The remaining 49 pts (median age 44 yrs, range: 19-65) were categorized into FDG-PET scan negative (31 pts) and positive (18 pts) groups. Each group was evaluated for event-free survival (EFS), which was defined as the interval between the date of the transplant to the date of relapse after complete remission (CR) or the date of progression for pts without CR or the date of death from any cause without a documented relapse. Results: The overall median follow-up was 14 mo (range: 2-58). There were no statistically significant differences in the distribution of lymphoma subtypes between the two groups. In the FDG-PET negative group, the median EFS was 19 mo (range: 2-59) with 18 pts (58%) remaining in CR. In the FDG-PET positive group, the median EFS was 5 mo (range: 1-19) with only 3 pts (17%) remaining in CR. Comparison between the two groups confirmed that the difference in the median EFS was highly statistically significant (p Conclusions: Our study suggests that a positive FDG-PET scan after salvage chemotherapy and prior to ASCT indicates an extremely poor chance of achieving a prolonged remission after ASCT. Clinical trials of new approaches should be investigated for pts with relapsed or primary refractory lymphoma that remains detectable by FDG-PET after salvage chemotherapy.
Valganciclovir for the treatment of cytomegalovirus infections in pediatric intestinal transplant recipients: A case series.

Background Cytomegalovirus (CMV) is the most common opportunistic infection post-transplant and is associated with significant morbidity and mortality. Currently, there are no FDA dosing recommendations for the use of valganciclovir for the treatment of CMV infections in pediatric patients. This case series describes the use of valganciclovir for the treatment of CMV infections in nine pediatric intestinal transplant recipients (pITR). Methods Retrospective review of pITR between January 2004 and December 2016. The primary outcome was resolution of CMV viremia. Secondary outcomes included time-to-resolution of viremia, relapse rate, incidence of resistance, hematologic adverse effects, rejection, graft loss, and death. Results Of 214 pITR, ten CMV infections were treated with valganciclovir. One patient was lost to follow-up while on treatment and was not included. Eight (89%) patients had resolution of CMV viremia. The average dose of valganciclovir was 14.3mg/kg (SD 0.82) twice daily. CMV resistance testing was completed in three (33.3%) patients; one patient had a documented mutation requiring leflunomide to clear viremia. Three (33.3%) patients experienced rejection within one month prior to or during treatment for CMV. Six (66.6%) experienced hematologic side effects. No patients died or experienced graft loss. Conclusion This is the first study to assess the use of valganciclovir for the treatment of CMV in pITR. Based on these results, weight-based dosing of valganciclovir seems to be an appropriate option for the treatment of CMV in pITR. Given limited number of patients reviewed in this case series and the high incidence of hematologic side effects, further investigation is warranted.
Structural Reliability Analysis of Marine Diesel Engine Shafting Systems: An Equivalent Stationary Process Approach to the Level Crossing Problem

This paper is concerned with the level crossing problem of a stress above some limit. The problem arises when the structural reliability of a diesel engine shafting system is examined. The first excursion failure probability is derived for the case that the stress on the shaft is a one-frequency cyclostationary random process. A new method is introduced where the cyclostationary random process is replaced with an equivalent stationary one, defined to have an envelope process with the same upcrossing rate as the envelope of the original cyclostationary process. Both processes are assumed to have the same probability of upcrossing a specific threshold. The agreement between this approach, which results in an analytical expression, and the "exact", computationally time-consuming "Markov approach" presented in earlier work is excellent.