cssi/SciSciGPT-SciSciNet huggingface dataset:
Zinc as an Imaging Biomarker of Prostate Cancer

Zinc has long been the focus of many biological investigations because of its essential role in biology including a catalytic role in many enzymes, a structural role in the many zinc finger proteins, and a physiological role in many secretory cell processes. Divalent zinc is known to be highly abundant in healthy prostate tissues and lower in prostate cancer (PCa). Given the need for newer diagnostic methods for detection of prostate cancer, zinc-responsive probes of various types have been considered as imaging tools for detecting tissue levels of zinc. Among them, recent zinc-responsive MRI probes show great promise for non-invasive detection of zinc ion secretion from the prostate and other tissues in vivo. In this review, we summarize the need for new diagnostic tools and demonstrate how responsive zinc probes and MRI could satisfy this unmet need.
Combination of carboplatin and intermittent normobaric hyperoxia synergistically suppresses benzo[a]pyrene-induced lung cancer.

Background/aims We explored the effects of intermittent normobaric hyperoxia alone or combined with chemotherapy on the growth, general morphology, oxidative stress, and apoptosis of benzo[a]pyrene (B[a]P)-induced lung tumors in mice. Methods Female A/J mice were given a single dose of B[a]P and randomized into four groups: control, carboplatin (50 mg/kg intraperitoneally), hyperoxia (95% fraction of inspired oxygen), and carboplatin and hyperoxia. Normobaric hyperoxia (95%) was applied for 3 hours each day from weeks 21 to 28. Tumor load was determined as the average total tumor numbers and volumes. Several markers of oxidative stress and apoptosis were evaluated. Results Intermittent normobaric hyperoxia combined with chemotherapy reduced the tumor number by 59% and the load by 72% compared with the control B[a]P group. Intermittent normobaric hyperoxia, either alone or combined with chemotherapy, decreased the levels of superoxide dismutase and glutathione and increased the levels of catalase and 8-hydroxydeoxyguanosine. The Bax/Bcl-2 mRNA ratio, caspase 3 level, and number of transferase-mediated dUTP nick end-labeling positive cells increased following treatment with hyperoxia with or without chemotherapy. Conclusions Intermittent normobaric hyperoxia was found to be tumoricidal and thus may serve as an adjuvant therapy for lung cancer. Oxidative stress and its effects on DNA are increased following exposure to hyperoxia and even more with chemotherapy, and this may lead to apoptosis of lung tumors.
A Review of the Role and Utility of Chest Computed Tomography in Penetrating Chest Trauma

Penetrating chest trauma is a major cause of morbidity and mortality in the USA, with changes in imaging techniques due to the advent of chest computed tomography. In this paper, we aim to review current literature and discuss indications for chest computed tomography (CCT) in the setting of hemodynamically stable patients with penetrating chest trauma. This review will also discuss the different injury patterns seen in thoracic and transmediastinal injuries and how CCT can aid in the identification of clinically relevant penetrating injuries. Chest computed tomography has proven to be more sensitive compared to traditional plain x-ray and other invasive modalities for many of the injury patterns associated with penetrating chest trauma. Where it fails, however, is in the diagnosis of esophageal injuries, where esophagoscopy and esophagography remain superior to current imaging techniques. More recently, CT esophagography has gained traction in diagnosing esophageal injuries associated with penetrating trauma. Although limited to a small prospective cohort, the use of CT esophagography appears promising and will likely play a larger role in the future. This review focuses on the current imaging trends for thoracic and transmediastinal injury patterns in penetrating chest trauma and discusses the indications and limitations of using chest computed tomography in these selected patients.
The Ever More Pressing Problem of Science Literacy

The causes of science illiteracy—the superficiality, misinformation, ignorance, and downright hostility toward science we encounter at virtually all levels of school and throughout adulthood—are numerous enough so that rooting out the problem will require a complex and sustained effort. But this is a war well worth fighting, and it is winnable as long as we choose our battles well, employ intelligent strategies and hang in there for the duration. As Winston Churchill exhorted his compatriots: “We will fight on the beaches, we will fight in the cities, we will never surrender!” (from “Getting High School Science in Order” by Leon Lederman.)
Stress intensities for nozzle cracks in reactor vessels

A series of six frozen stress photoelastic tests was conducted to investigate the distribution of stress-intensity factor (SIF) along a crack which occurred at the juncture of a pipe (nozzle) with a cylindrical pressure vessel. Typical photoelastic-fringe patterns are shown for slices which were taken mutually orthogonal to the flaw border and the flaw surface. A typical plot of normalized apparent SIF vs. square root of normalized distance from the crack tip is presented. The variation in SIF along the flaw border is given for all six different crack geometries and, also, the variation of SIF with varyinga/T is presented.
Light/Laser Applications in Gynecology

The use of CO2 laser in the treatment of uterine cervical intraepithelial lesions is well established and indications, as well as techniques, have changed very little for over 30 years. The Cochrane Systematic Review from 2000 suggests no obviously superior technique. CO2 laser ablation of the vagina is also established as a safe treatment modality for VAIN (Vaginal Intraepithelial Neoplasia), and has been used extensively in the treatment of VIN (Vulvar Intraepithelial Neoplasia) and lower genital tract condylomata acuminata. CO2 laser permits treatment of lesions with excellent cosmetic and functional results. The treatment of heavy menstrual bleeding by destruction of the endometrial lining using various techniques, including Nd:YAG laser ablation, has been the subject of a 2002 Cochran Database Review. Among the compared treatment modalities are modified laser techniques. The conclusion by reviewers is that outcomes and complication profiles of newer techniques compare favorably with the gold standard of endometrial resection. Myoma coagulation or myolysis with Nd:YAG laser through the laparoscope or hysteroscope is a conservative treatment option for women who wish to preserve their child bearing potential.
Free energy of hydration and heat capacity of calcium dipicolinate in Bacillus spore cores

Wet heat treatments are widely used sterilization techniques for inactivating dangerous and resistant sporulating bacteria. The effectiveness of such treatments depends upon the thermodynamics of water uptake by the spore as well as the kinetics of phase transformations in the hydrated spore core. The mechanism behind these chemical and physical processes remains unknown because the thermodynamic properties of the spore core constituents are not well understood. Here, we use reactive molecular dynamics simulations to calculate the vibrational density of states and specific heat of hydrated calcium dipicolinate as well as the free energy of hydration based on Jarzynski's inequality. These two quantities are used to construct a phase diagram of hydrated calcium dipicolinate, indicating the extent of hydration at different pressures and temperatures, which can be used to identify potential regimes for wet-heat sterilization of bacterial spores.Wet heat treatments are widely used sterilization techniques for inactivating dangerous and resistant sporulating bacteria. The effectiveness of such treatments depends upon the thermodynamics of water uptake by the spore as well as the kinetics of phase transformations in the hydrated spore core. The mechanism behind these chemical and physical processes remains unknown because the thermodynamic properties of the spore core constituents are not well understood. Here, we use reactive molecular dynamics simulations to calculate the vibrational density of states and specific heat of hydrated calcium dipicolinate as well as the free energy of hydration based on Jarzynski's inequality. These two quantities are used to construct a phase diagram of hydrated calcium dipicolinate, indicating the extent of hydration at different pressures and temperatures, which can be used to identify potential regimes for wet-heat sterilization of bacterial spores.
Sequential phases of RGC axonal and somatic injury in EAE mice examined using DTI and OCT.

Abstract Background Clinical imaging modalities including optical coherence tomography (OCT) and diffusion tensor imaging (DTI) are vital in Multiple Sclerosis (MS), but their relationships during the different phases of Retinal ganglion cell (RGC) degeneration are not clear. We hypothesize that initial injury in optic nerve causes axonal degeneration leading to RGC loss in retina, which can be characterized by a combination of DTI and OCT. Our objective was to examine the correlation between noninvasive and histological data to chronicle the degeneration profile of RGCs in the retina and optic nerve in a mouse model of MS. Materials and methods Experimental Autoimmune Encephalomyelitis (EAE) was induced in 11 C57Bl/6 mice, with 8 mice reserved as controls. OCT and DTI was conducted 2–8 weeks after induction of EAE. The thickness of the retinal ganglion cell complex (GCC) was measured using OCT and compared to DTI indices measured in optic nerves. End-stage histology was used to quantify axon/myelin loss in the optic nerve and retinal thinning/RGC loss in the retina. Results Significant changes in DTI-derived Axial Diffusivity (AD, −17.2%) and Trace Diffusivity (TR, −18.3%) began after 2 weeks of EAE. Later significant reductions in Fractional Anisotropy (FA) and AD, with increases in Radial Diffusion (RD) were apparent after 4 and 8 weeks. OCT-derived measures of GCC thickness were reduced after 4 weeks, and reached significant reduction after 8 weeks. Among EAE mice, DTI (FA, AD and RD measures) and OCT measures were all significantly correlated after 4 and 8 weeks. Among histology measures, RGC density (−23%), RGC size (−27%), and the number of SMI31+ axons (−54%) were reduced significantly. DTI measures of FA and AD along with GCC thinning were the best independent predictors of axon loss. Conclusions DTI and OCT measures are tightly correlated during the chronic phase of axonal degeneration (4–8 weeks) in EAE mice. After 8 weeks of EAE, both OCT and DTI measures are strong predictors of axon loss in the Optic Nerve.
Cross-acceleration and the relationship between board independence and bond yield spreads

Abstract This paper investigates the mediating effect of cross-acceleration provisions in bond debt on board independence and bond yield spreads. Cross-acceleration provisions cause bond debt to accelerate if other debt (mainly bank debt) is accelerated and allows bondholders to benefit from the monitoring of fellow creditors. Board independence, while generally seen as a positive governance feature, has been viewed as detrimental to bondholder interests when bondholder-shareholder conflicts are high. Cross-acceleration works to protect bondholder interests through increased likelihood of bankruptcy court supervision (or early repayment of debt). Consistent with this view, we find that when bondholder-shareholder conflict are high bonds issued without cross-acceleration provisions have yields that increase in board independence whereas bonds issued with cross-acceleration have yields that decrease in board independence. The results suggest that cross-acceleration plays a role in mitigating the tendency of more independent boards to favor shareholders when bondholder-shareholder conflicts arise.
Somatic and germline genomics in paediatric acute lymphoblastic leukaemia

Advances in genomic research and risk-directed therapy have led to improvements in the long-term survival and quality of life outcomes of patients with childhood acute lymphoblastic leukaemia (ALL). The application of next-generation sequencing technologies, especially transcriptome sequencing, has resulted in the identification of novel molecular subtypes of ALL with prognostic and therapeutic implications, as well as cooperative mutations that account for much of the heterogeneity in clinical responses observed among patients with specific ALL subtypes. In addition, germline genetic variants have been shown to influence the risk of developing ALL and/or the responses of non-malignant and leukaemia cells to therapy; shared pathways for drug activation and metabolism are implicated in treatment-related toxicity and drug sensitivity or resistance, depending on whether the genetic changes are germline, somatic or both. Indeed, although once considered a non-hereditary disease, genomic investigations of familial and sporadic ALL have revealed a growing number of genetic alterations or conditions that predispose individuals to the development of ALL and treatment-related second cancers. The identification of these genetic alterations holds the potential to direct genetic counselling, testing and possibly monitoring for the early detection of ALL and other cancers. Herein, we review these advances in our understanding of the genomic landscape of childhood ALL and their clinical implications. Herein, advances in our understanding of the genomic landscape of childhood acute lymphoblastic leukaemia (ALL), encompassing both somatic and germline alterations, are reviewed. The clinical implications of these alterations, particularly those in the germ line, are discussed with regard to susceptibility to ALL, treatment responses and therapy-related toxicities.
Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming

Eukaryotic cell homeostasis requires transfer of cellular components among organelles and relies on membrane fusion catalyzed by SNARE proteins. Inactive SNARE bundles are reactivated by hexameric N-ethylmaleimide-sensitive factor, vesicle-fusing ATPase (Sec18/NSF)-driven disassembly that enables a new round of membrane fusion. We previously found that phosphatidic acid (PA) binds Sec18 and thereby sequesters it from SNAREs and that PA dephosphorylation dissociates Sec18 from the membrane, allowing it to engage SNARE complexes. We now report that PA also induces conformational changes in Sec18 protomers and that hexameric Sec18 cannot bind PA membranes. Molecular dynamics (MD) analyses revealed that the D1 and D2 domains of Sec18 contain PA-binding sites and that the residues needed for PA binding are masked in hexameric Sec18. Importantly, these simulations also disclosed that a major conformational change occurs in the linker region between the D1 and D2 domains, which is distinct from the conformational changes that occur in hexameric Sec18 during SNARE priming. Together, these findings indicate that PA regulates Sec18 function by altering its architecture and stabilizing membrane-bound Sec18 protomers.
Disability, self-rated health, and time seeking medical care.

Abstract Background Population-level estimates of patient-reported time seeking medical care in the United States by disability status are unknown. Objective To estimate the likelihood of seeking medical care on an average day and the number of minutes spent traveling to, waiting for, and receiving medical care among those receiving care, by disability status. Methods Data are analyzed from the nationally representative 2008, 2010, and 2012–2016 American Time Use Surveys. Weighted logistic and linear regression models evaluate the association between sensory, cognitive, physical, or multiple disabilities and time spent seeking medical care, net of age, sex, race/ethnicity, education, employment, nativity, marital status, parental status, income, metropolitan area, and self-rated health. Results The presence of a disability positively associates with the likelihood of seeking medical care on an average day. Patients with disabilities spend more total time in medical care than patients without disabilities as a result of longer clinical and travel time. These differences cannot be explained by sociodemographic disparities or by poorer self-rated health. Conclusions Patient time burden is exacerbated by the presence of a disability. It is important to consider disability status along with other social disparities when evaluating the delivery of timely and equitable care.
Defect engineering of phase-change materials for ultralow-power electronics and optoelectronics (Conference Presentation)

Phase-change electronic memory utilizes the electric field-induced reversible structural change in chalcogenide materials to switch between crystalline and amorphous phases to store information, which is fast and non-volatile. In spite of extensive investigations of the field-induce phase-change phenomena, the underlying mechanisms are quite complex and their elucidation requires the continued development of new experimental tools. Our group has demonstrated that conventional understanding of melt-quench based amorphization process needs to be revisited. While working with single-crystalline nanowires which due to their long lengths do not typically reach high temperatures required for conventional melting of the material, we realized that alternate pathways for crystal-amorphous transformation can exist. Furthermore, nanowires due to their cylindrical geometry, conventional melting should lead to the formation of an amorphous shell around the crystalline core, which cannot explain the abrupt resistance switching as observed. We have shown that crystal-amorphous transformation in phase-change materials can be achieved through a subtle and ad lower energy costing defect-based pathway. This pathway involves creation of extended defects such as anti-phase boundaries (APBs) in GeTe and dislocations in Ge2Sb2STe5, which migrate and accumulate at a region of local inhomogeneity creating a defect template. The formation of APBs leads to polar domain inversion as revealed by optical second-harmonic generation polarimetry. Due to the accumulation of defects locally, the material first undergoes a metal-to-insulator transition followed by a structural collapse leading to amorphization without conventional melting. We utilized this understanding to pre-induce defects in the crystalline phase via controlled ion bombardment to engineer carrier localization and enhance carrier-lattice coupling in order to efficiently extract work required to introduce bond-distortions necessary for amorphization from input electrical energy itself. We demonstrated that such a strategy shows 100X improvement in amorphization current densities compared to the melt-quench strategy. The existence of multiple resistance states along with ultra-low power switching makes this approach promising for low power memory and neuromorphic computation. We will also discuss our efforts to integrate defect-engineered phase change nanowires in integrated photonics platforms for designing the next generation of reconfigurable photonic devices. References [1] S.W.Nam et al., Science 2012, 336, 1561. [2] P.Nukala et al., Nano Lett. 2014, 14, 2201. [3] P. Nukala et al., Nature Communications, 2016, 7, 10482. [4] P. Nukala et al., Nature Communications, 2017, 8, 15033.
Do Genetic Differences Explain the Ability of an Alkaline Shrub to Grow in Both Uplands and Wetlands

The hydrophyte Allenrolfea occidentalis (S. Watson) Kuntze (iodinebush) is a halophytic shrub of the arid southwest that is listed as a facultative wetland species on the National Wetland Plant List. This rating means that the species is usually a hydrophyte but occasionally is found in uplands. We tested for genetic (ecotypic) differences between plants sampled from wetlands versus uplands. We used the technique of genotyping by sequencing to generate data from 132 plants from 30 locations representing both wetland and upland occurrences for over 1300 loci. Analyses indicated that the strongest genetic signal is from differences in geographic distribution: samples that are in close geographic proximity tend to be more similar genetically regardless of whether they occur in wetland or upland locations. We detected no effect of habitat on overall genetic structure, and we found only 2 (of the 1381) loci with a positive association between genotype and habitat; in both cases the association was very weak. We infer that A. occidentalis occurrences near or in wetlands are not influenced by significant differences in genetics, and we find no evidence for wetland and upland ecotypes of this species.
Ozone Trends from Satellite Data

Ozone absorbs ultraviolet, visible, and infrared radiation. Through these absorption processes ozone plays an important role in the radiation balance of the atmosphere, and thus changes in ozone could lead to effects on radiation balance and climate. The global distribution of ozone has been measured from satellites since November, 1978. Significant down ward trends in the northern mid and high latitude total ozone amount have been deduced from this data. Recent analyses have shown that the total ozone at middle and high latitudes in 1992 and 1993 was anomalously low (by a few percent) even when compared to a continued down ward trend modulated by the QBO and solar cycle. The trend in total ozone at mid and high latitudes has been shown to be an effect occurring primarily in the lower stratosphere. Near the equator, no statistically significant trends in total ozone have been observed. It is not yet clear what altitude dependent changes may have occurred near the equator.
Impact of Protocol Based Fluid Resuscitation in Heart Failure Patients Admitted with Sepsis

Introduction Sepsis (severe sepsis and septic shock) with co-existing cardiovascular dysfunction is associated with increased mortality. With concomitant heart failure (HF), clinicians tend to limit fluid resuscitation in sepsis patients due to concerns of pulmonary edema and respiratory failure. We attempted to determine the effect of protocolized fluid resuscitation as per Surviving Sepsis Campaign Guidelines in sepsis patients with HF on clinical outcomes. Methods This was a single center, retrospective study of patients aged ≥18 years, admitted to a critical care unit with sepsis, having a co-diagnosis of systolic HF (EF Results 63 patients received fluids based on clinical judgement (2013), and 54 patients received protocolized fluids (2017). Both groups had similar patient demographics and co-morbidities. In-hospital mortality was higher in 2013, compared to 2017 [49 vs 41%, OR 0.7 (95% CI 0.3,1.5) p=0.36]. Lactic acid ≥4mmol/L was significantly associated with increased mortality [66 vs 36%, OR 3.5 (95% CI 1.6,8.1) p=0.002]. We found no difference in length of stay between the two groups. Patients with coronary artery disease, diabetes mellitus, hypertension, chronic obstructive pulmonary disease and cancer had higher absolute mortality. Conclusion This study demonstrates that there was no difference in-hospital mortality or critical care length of stay between patients receiving protocolized fluid resuscitation and patients receiving fluid resuscitation based on clinical judgement. Further prospective studies in a larger sample of patients are required to support these findings.
Tumor T2 signal intensity and stalk angulation correlates with endocrine status in pituitary adenoma patients: a quantitative 7 tesla MRI study.

Pituitary adenomas are common CNS tumors that can cause endocrine dysfunction due to hormone oversecretion and by mass effect on the normal gland. The study of pituitary adenomas and adjacent sellar anatomy with high-resolution 7 T MRI may further characterize endocrine dysfunction. The purpose of this study was to determine the efficacy of 7 T MRI in identifying radiological markers for endocrine function. MR images obtained in 23 patients with pituitary adenomas were reviewed by consensus between three neuroradiologists. Landmarks and criteria were devised to measure radiological features of stalk, tumor, and normal gland. Fischer’s exact tests and nominal logistic regression were performed. Mean cross-sectional area of the stalk just below the infundibular recess was 6.3 ± 3.7 mm2. Mean curvature and deviation angles were 34.2° ± 23.2° and 29.7° ± 17.3°, respectively. Knosp scores obtained differed between 7 T and lower field strength scans (P < 0.0001 [right] and P = 0.0006 [left]). Ability to characterize tumor was rated higher at 7 T compared with lower field MRI, P = 0.05. Confidence in visualizing normal gland was also higher using 7 T MRI, P = 0.036. The six hormone-secreting tumors had higher corrected T2 mean SI than non-secreting tumors (2.54 vs. − 0.38, P = 0.0196). Seven patients had preoperative hypopituitarism and had significantly greater stalk curvature angles than patients without hypopituitarism (71.7° vs. 36.55°, P = 0.027). Radiological characterization of pituitary adenomas and adjacent native pituitary tissue may benefit with the use of 7 T MRI. Corrected T2 SI of tumor may be a sensitive predictor of hormonal secretion and may be useful in the diagnostic work-up for pituitary adenoma. 7 T MRI may be valuable in identifying markers of endocrine function in patients with pituitary adenomas. Our results indicate that hormone-secreting tumors have higher T2-weighted SI and tumors associated with preoperative hypopituitarism have greater stalk curvature angles.
Sea Ice Thickness Measurement Using Spaceborne GNSS-R: First Results With TechDemoSat-1 Data

In this article, an effective schematic is developed for estimating sea ice thickness (SIT) from the reflectivity ( $\Gamma$ ) produced with TechDemoSat-1 (TDS-1) Global Navigation Satellite System-Reflectometry data. Here, $\Gamma$ is formulated as the product of the propagation loss due to SIT and the reflection coefficient of underlying seawater. The effect of surface roughness on $\Gamma$ is neglected when only considering signals of coherent reflection. In practice, $\Gamma$ at the specular point is first generated using TDS-1 data. Afterwards, SIT is calculated from TDS-1 $\Gamma$ based on the proposed reflectivity model, and verified with two sets of reference SIT data; one is obtained by the Soil Moisture Ocean Salinity (SMOS) satellite, and the other is the combined SMOS/Soil Moisture Active Passive (SMAP) measurements. This analysis is performed on the data with SIT less than 1 m. Through comparison, good consistency between the derived TDS-1 SIT and the reference SIT is obtained, with a correlation coefficient ( $r$ ) of 0.84 and a root-mean-square difference (RMSD) of 9.39 cm with SMOS, and an $r$ of 0.67 and an RMSD of 9.49 cm with SMOS/SMAP, which demonstrates the applicability of the developed model and the utility of TDS-1 data for SIT estimation. In addition, this method is proved to be useful for improving existing sea ice detection accuracy.
Water Promotion (or Inhibition) of Condensation Reactions Depends on Exposed Cerium Oxide Catalyst Facets

Nanoparticles with well-defined facets enable quantitative correlations between surface features and catalytic activity. Here, we explore the role of geometric and acid–base properties in the mecha...
MM-239: A Tertiary Center Experience of Multiple Myeloma Patients with COVID-19: Lessons Learned and the Path Forward

Context: The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has resulted in over 100,000 deaths in the United States. Our institution has treated over 2,000 COVID-19 patients during the pandemic in New York City. Objective: We explored the population of myeloma patients who developed COVID-19 to identify risk factors tied to poor outcomes. Design: We performed a retrospective study of a cohort of 58 patients with a plasma cell disorder (54 MM, 4 smoldering MM) who developed COVID-19 between March 1, 2020 and April 30, 2020. We report epidemiological, clinical, and laboratory characteristics, including persistence of viral detection by polymerase chain reaction (PCR) and anti-SARS-CoV-2 antibody testing, treatments initiated, and outcomes. Setting: A large tertiary care cancer center in New York at the epicenter of the COVID-19 pandemic in the USA. Patients: Patient charts were analyzed retrospectively. Patients had MM or SMM and COVID-19. Results: Of the 58 patients diagnosed with COVID-19, 36 were hospitalized and 22 were managed at home. The median age was 67 years; 52% of patients were male, and 63% were non-white. Hypertension (64%), hyperlipidemia (62%), obesity (37%), diabetes mellitus (28%), chronic kidney disease (CKD, 24%), and lung disease (21%) were the most common comorbidities. In the total cohort, 14 patients (24%) died. Older age (>70 years), male sex, and cardiovascular risk were significantly (p Conclusions: Drug exposure and MM disease status at the time of contracting COVID-19 had no bearing on patient outcome. Mounting a severe inflammatory response to SARS-CoV-2 and severe hypogammaglobulinemia were associated with higher mortality. These findings pave a path to the identification of vulnerable patients who need early intervention to improve outcomes of myeloma patients in future outbreaks of COVID-19. The majority of myeloma patients mounted a specific antibody response to SARS-CoV-2.
Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework

We have formulated a Riemannian framework for describing the geometry of collective vari-able spaces of biomolecules within the context of molecular dynamics (MD) simulations. Theformalism provides a theoretical framework to develop enhanced sampling techniques, path-findingalgorithms, and transition rate estimators consistent with a Riemannian treatment of the collec-tive variable space, where the quantities of interest such as the potential of mean force (PMF)and minimum free energy path (MFEP) remain invariant under coordinate transformation. Spe-cific algorithms within this framework are discussed such as the Riemannian umbrella sampling,the Riemannian string method, and a Riemannian-Bayesian estimator of free energy and diffusionconstant, which can be used to estimate the transition rate along an MFEP
Criticality assessment for a regional maritime economy

Objective: To identify and assess the criticality for infrastructure assets and better understand their dependencies, interdependencies, and supply chain reliance. Design: This study used a modified mission impact, symbolism, history, accessibility, recognizability, population, and proximity model combined with a deliberative process with regional subject matter experts. Setting: Hampton roads Virginia maritime area. Participants: Emergency managers, US Corps of Engineers, US Coast Guard, law enforcement, railroad industry, intelligence community, Virginia Department of Emergency Management, Virginia Department of Transportation, and Virginia Port. Main outcome: A prioritized list of one-to-n critical assets in the maritime area and identification of up and downstream dependencies. Results: The final most highly critical grouping included 26 out of 277 assets including especially important road bridges and tunnels, rail bridges and choke points, shipping channels, and marine terminals. Conclusions: Subject matter experts identified 277 critical infrastructure assets in the Hampton Roads Maritime Area (HRMA). From these, 26 assets that were deemed to be significantly more critical than others. From this reduced list, 12 were further assessed to be most important. The selection process provided significant support to those responsible for providing protection, mitigating potential damage, and planning recovery and allows informed, objective expenditures of limited funding. Additional key findings include the following: Proximity, or the potential for an asset that has been damaged or destroyed to cause direct harm to adjacent assets in the surrounding community, drives criticality in the HRMA more than any other factor in the model . A small group of 26 out of 277 assets exerts an outsized impact in the HRMA—nearly 20 percent of criticality—due to the potential consequences associated with their destruction or disruption . Road transportation, particularly tunnels, represents the primary dependency among critical assets. Major road and maritime transportation assets rely heavily on federal and state organizations to maintain their function . Supply chain: The critical asset group supports or supplies many missions and industries both nationally and internationally, including defense, manufacturing, commercial enterprise, and the movement of raw commodities .
Emerging Capabilities for the High-Throughput Characterization of Structural Materials

Structural materials have lagged behind other classes in the use of combinatorial and high-throughput (CHT) methods for rapid screening and alloy development. The dual complexities of composition a...
The sharing economy: Implications for revenue management

The ‘sharing economy’ has emerged in the past several years as a new model for offering a variety of goods and services, often in a peer-to-peer environment. As the sharing economy grows, it presents both threats and opportunities for revenue management.
Neural Mechanisms That Lead to Apnea

During apneas or hypopneas in sleep there are intermittent reductions in the activity of the upper airway muscles (obstructive apnea) or of the respiratory pump muscles such as the diaphragm (central apnea). Although anatomical abnormalities in the upper airway can predispose subjects to development of apnea, presumably by magnifying the mechanical effects of reduced activity of the upper airway muscles, important to our understanding of the pathogenesis of apnea is determining the mechanisms that produce intermittent inhibition or disfacilitation of the respiratory muscles during sleep. In this chapter we discuss our current understanding of the mechanisms that produce this reduction in neural activity in both non-rapid eye movement sleep (non-REM) and rapid eye movement sleep (REM). It is our thesis that the neural mechanisms that lead to apnea are different in these states.
The host range of herpes simplex virus: Interferon, viral DNA, and antigen synthesis in abortive infection of dog kidney cells

Abstract Herpes simplex virus strain MP (HSV-MP) and pseudorabies virus (PSV) multiply in HEp-2 cells. In dog kidney cells PSV multiplies, whereas HSV-MP fails to multiply or to produce plaques. HSV-MP interferes with the multiplication of PSV in HEp-2 cells and in dog kidney cells. Studies of dog kidney cells exposed to HSV-MP revealed that these cells (1) produce viral antigen, interferon, and small amounts of DNA characteristic of HSV-DNA, (2) do not form particles with physical characteristics of HSV-MP, and (3) show signs of infection and fail to multiply. The significance of the data is discussed.
What mad pursuit?: Obsessive relational intrusion and stalking related phenomena

The topics of stalking and obsessive relationship pursuit rapidly have gained the attention of social scientists, clinicians, and law enforcement professionals alike. This review takes stock of the burgeoning multidisciplinary literature in this area. The development of the concept of stalking and its corresponding literature is charted, delineating and contrasting the clinical/forensic and interactional/relational perspectives. The review and synthesis of current scholarship yields key conclusions regarding the incidence of stalking and obsessive relational intrusion (ORI), the various tactics and motives of stalkers and obsessive pursuers, and the consequences for victims. Further, a comprehensive typology of victim coping responses is presented, along with a sampling of theoretical frameworks designed to help explain perpetration and victimization. Several avenues for future investigation are proposed.
A dietitian-delivered group nutrition program leads to reductions in dietary fat, serum cholesterol, and body weight: the Worcester Area Trial for Counseling in Hyperlipidemia (WATCH).

Abstract Objective To assess the effectiveness of a dietitian-based nutrition counseling and education program for patients with hyperlipidemia. Design A 4-session program implemented as a complement to a randomized physician-delivered intervention. Subjects/setting From 12 practice sites of the Fallon Clinic, 1,162 subjects with hyperlipidemia were recruited, 645 of whom had data sufficient for our primary analyses. Intervention Two individual and 2 group sessions conducted over 6 weeks. Main outcome measures Total and saturated fat levels; serum low-density lipoprotein cholesterol levels; and body weight, measured at baseline and after 1 year. Statistical analyses Multiple linear regression was used to evaluate changes in outcome measures. Results After 1 year, there were significant reductions in outcome measures for subjects attending 3 or 4 nutrition sessions vs subjects attending fewer than 3 sessions or those never referred to a nutrition session. Reductions (mean± standard error) in saturated fat (measured as percent of energy) were 2.7±0.5%, 2.1±0.5%, and 0.3±0.1%, respectively. These reductions correspond to roughly a 22% relative change from baseline in those attending 3 or 4 sessions. Corollary reductions were observed for total fat (measured as percent of energy): 8.2±1.4%, 5.0±1.4%, and 0.7±0.4%; low-density lipoprotein cholesterol: 0.48±0.11mmol/L, 0.13±0.11mmol/L, and 0.02±0.03mmol/L; and body weight: 4.5±0.9kg, 2.1±0.8kg, and 1.1±0.2kg. The specified changes were additive to those of the physician-delivered intervention. Applications/conclusions This investigation provides empirical data demonstrating the effectiveness of a dietitian-delivered intervention in the care of patients with hyperlipidemia. J Am Diet Assoc. 1999;99:544–552.
Efficient computation of frequent and top-k elements in data streams

We propose an integrated approach for solving both problems of finding the most popular k elements, and finding frequent elements in a data stream. Our technique is efficient and exact if the alphabet under consideration is small. In the more practical large alphabet case, our solution is space efficient and reports both top-k and frequent elements with tight guarantees on errors. For general data distributions, our top-k algorithm can return a set of k′ elements, where k′ ≈ k, which are guaranteed to be the top-k' elements; and we use minimal space for calculating frequent elements. For realistic Zipfian data, our space requirement for the frequent elements problem decreases dramatically with the parameter of the distribution; and for top-k queries, we ensure that only the top-k elements, in the correct order, are reported. Our experiments show significant space reductions with no loss in accuracy.
High Resolution Two-Photon Spectroscopy of Rb Rydberg Levels

In this paper we report on our investigation of the interesting features, and problems, associated with ultrahigh resolution two-photon spectroscopy, using a frequency controlled dye laser to study the 52S-n2S transitions in rubidium. The optical Ramsey technique of separated interactions is used to reduce transit broadening. Narrow resonances of 17 kHz full width half maximum are observed.
Picosecond Switching in Josephson Tunnel Junctions

We report experimental and numerical studies of the dynamics of the Josephson tunnel junction driven by picosecond current pulses. Both single pulse switching, and the response to the train of pulses are discussed. The observed behavior is explained in terms of the “ccritical pulse charge” concept.
50 – Female Infertility and Assisted Reproductive Technology

Approximately 50 to 60% of couple infertility is because of a female factor, while male factors account for another 40 to 50% of infertility. This chapter mainly addresses female infertility. Among female factors for infertility, about 40% are anatomic reasons (uterine and tuboperitoneal diseases), while another 40% reason can be ovulatory dysfunction. Other factors may include immunologic factors, impenetrable cervical mucous, luteal phase defect, or medical conditions (e.g., diabetes mellitus), which may interfere with implantation. Uterine defects can be identified by hysterosalpingogram (HSG), saline infusion sonography, or hysteroscopy. Hysterosalpingogram has traditionally been the gold standard for tubal evaluation. Laparoscopy, however, has the advantage of more precise observation and documentation. Appropriate sperm-cervical mucus interaction is necessary for spontaneous conception, which is determined by post coital test. Adequacy of the luteal phase can be measured by the sum of three postovulatory progesterone levels (days 5, 7, and 9 postovulation). An endometrial biopsy is the gold standard. Thyroid disorders, particularly hypothyroidism, may be associated with anovulation. Thyroid-stimulating hormone (TSH) should be screened and thyroid supplements administered where appropriate.
On state space formulation of scattering Schur property of two-dimensional polynomials

Lyapunov characterization of the scattering Schur property of multidimensional polynomials is given. It is shown that the notion of modal observability of two-dimensional systems is a necessary ingredient of such a description. A nontrivial example is given to illustrate the result. >
Acute and Chronic Airway Disease After Human Respiratory Syncytial Virus Infection in Cotton Rats (Sigmodon hispidus)

Infection with respiratory syncytial virus (RSV) generally presents as a mild, upper airway disease in human patients but may cause severe lower airway disease in the very young and very old. Progress toward understanding the mechanisms of RSV pathogenesis has been hampered by a lack of relevant rodent models. Mice, the species most commonly used in RSV research, are resistant to upper respiratory infection and do not recapitulate the pattern of virus spread in the human host. To address the need for better rodent models of RSV infection, we have characterized the acute and chronic pathology of RSV infection of a relatively permissive host, cotton rats (Sigmodon hispidus). We demonstrate that virus delivered to the upper airway results in widespread RSV replication in the ciliated respiratory epithelial cells of the nasal cavity and, to a lesser extent, of the lung. Although acute inflammation is relatively mild and rapidly eliminated after viral clearance, chronic, eosinophilic lung pathology persists. These data support the use of cotton rats as a robust rodent model of human RSV disease, including the association between RSV pneumonia and subsequent development of allergic asthma.
Delayed primary anastomosis for esophageal atresia: 18 Months' to 11 years' follow-up

In 1977 we started treating babies with isolated esophageal atresia by delayed primary anastomosis and in 1981 reported our early experience in five cases treated between 1977 and 1979. Since 1979, 11 further consecutive cases have been managed by initial gastrostomy followed by delayed primary esophageal anastomosis. Their mean gestation was 35 weeks (range, 28 to 40 weeks) and mean birth weight was 2,040 g (range, 1,140 to 2,720 g). The esophageal gap between the two ends when assessed initially at fluoroscopy ranged from 2.2 to 4.5 cm (mean, 3.2 cm). Age at delayed primary anastomosis ranged from 6 to 20 weeks. Anastomotic leak occurred in three babies in the immediate postoperative period and all were successfully managed conservatively. Eight of the 11 patients developed anastomotic strictures; seven cases required 1 to 5 esophageal dilatations. One patient who did not respond to multiple esophageal dilatations required resection of an esophageal stricture. One patient died at 15 months of age of unrelated causes. The 10 surviving patients have been followed-up from 18 months to 11 years. At follow-up, seven patients were eating normally. Three patients had swallowing difficulties and all three were found to have esophageal strictures on barium swallow, two of them also had gross esophageal reflux and hiatus hernia. The height and weight in the 10 patients varied from 3rd centile to 75th centile. Delayed primary anastomosis is feasible in cases of isolated esophageal atresia and the patient's own esophagus is the best. A more aggressive approach should be applied to gastroesophageal reflux in these patients.
Trace Element Composition of Fertilizers and Soil Amendments

The use of fertilizers and soil amendments has raised concern regarding the toxic accumulation of their trace components in the environment. The objective of this research was to evaluate the trace element and heavy metal composition of a wide variety of fertilizers and soil amendments. Thirty-five elements, including priority pollutants, were determined in 24 materials. A microwave HNO 3 -HF-H 2 O 2 -H 3 BO 3 digestion procedure was used to dissolve the samples. Selected solid samples were directly analyzed by neutron activation analysis, while atomic absorption and inductively-coupled plasma atomic emission spectrometric determinations were carried out on the digests. The trace element and heavy metal concentrations generally decreased in the following sample order: rock phosphate > sewage sludge > phosphorus fertilizer > organic amendments and liming materials > K fertilizers > N fertilizers. Relatively high concentrations of toxic elements in the sewage sludge, rock phosphate, and phosphorus fertilizer samples suggest that these materials should be the primary target materials for environmental evaluations.
Correlating Selective Supercritical Fluid Extraction with Bioremediation Behavior of PAHs in a Field Treatment Plot

Selective supercritical fluid extraction (SFE) behavior of PAHs from manufactured gas plant (MGP) site soils was determined on untreated soil and on soils collected after 1/2 year and 1 year of bioremediation in a field land treatment plot. Sequentially stronger SFE conditions gave selective extraction of PAHs associated with “fast” (or “rapidly desorbing”), “moderate,” “slow,” and “very slow” sites on the soil collected before and during bioremediation. While all PAHs from the untreated soil showed “stair-step” extraction curves (with molecules in each of the four “fast” to “very slow” SFE fractions), two- and three-ring PAHs were found mostly in the “fast” fraction, while the five- and six-ring PAHs were found almost completely in the “slower” fractions. SFE comparisons of the untreated and bioremediated soils showed that bioremediation only removed PAH molecules which were found in the “fast” fractions by SFE and that remediation for 1 year did not result in the migration of PAHs from “slower” to “fast...
Food limited survival of larval razorback sucker, Xyrauchen texanus, in the laboratory

Razorback suckers in Lake Mohave, Arizona-Nevada, are suffering recruitment failure. Concomitantly, lake zooplankton levels are low and variable. We test, under laboratory conditions, the possibility that starvation is a cause of low recruitment. Razorback sucker larvae that were starved, received food too late, or were provided with insufficient food died between 20 and 30 d after hatching. Yolk absorption was at ∼ 8d after hatching, the critical period during which larvae must feed or most will die lies between ∼ 8 and 19d, and the point of irreversible starvation for individuals is between 19 and 23 d after hatching. Results support food-related mortality as a contributor to year-class failure of razorback sucker in Lake Mohave.
Reorganizing Large Web Sites

(2001). Reorganizing Large Web Sites. The American Mathematical Monthly: Vol. 108, No. 1, pp. 16-27.
Linear programming with multiple choice constraints for single chain undiscounted Markov decision problems

This paper develops an efficient LP algorithm for solving single chain undiscounted Markov decision problems. The algorithm imposes, in the framework of the simplex method, the multiple choice constraints that exactly one basic variable be chosen from each Markov state. It is proved that the algorithm converges to an optimal solution in a finite number of steps.