cssi/SciSciGPT-SciSciNet huggingface dataset:
An automated homology-based approach for identifying transposable elements

Background Transposable elements (TEs) are mobile sequences found in nearly all eukaryotic genomes. They have the ability to move and replicate within a genome, often influencing genome evolution and gene expression. The identification of TEs is an important part of every genome project. The number of sequenced genomes is rapidly rising, and the need to identify TEs within them is also growing. The ability to do this automatically and effectively in a manner similar to the methods used for genes is of increasing importance. There exist many difficulties in identifying TEs, including their tendency to degrade over time and that many do not adhere to a conserved structure. In this work, we describe a homology-based approach for the automatic identification of high-quality consensus TEs, aimed for use in the analysis of newly sequenced genomes.
Motion and force control for multiple cooperative manipulators

The authors address the problem of motion and force control of multiple robot arms manipulating an object. A general control paradigm that decouples the motion and force control problems is introduced. For motion control, different control strategies are constructed on the basis of control input variables. There are three natural choices: joint torques, arm tip force vectors, and the acceleration of a generalized coordinate. The first choice allows relatively model-independent control by exploiting the Hamiltonian structure of the open-loop system. The latter two require the full model information but produce simpler control design problems. The motion control determines the joint torque only to within a manifold, owing to the multiple-arm kinematic constraint. To resolve the nonuniqueness of the joint torques, two methods are introduced. If the arm and object models are available, the allocation of the desired end-effector control force to the joint actuators can be optimized. The other possibility is to control the internal force about some set point. Effective force regulation can be achieved with little model information. >
On-resonant trion Rabi oscillations and spin quantum beats in a singly charged InAs quantum dot

We demonstrate, to our knowledge, the first coherent transient measurements of a single self-assembled InAs quantum dot charged with a single electron. The measurements show both trion Rabi oscillations and spin quantum beats.
A Young Woman With Heart Failure and Altered Mental Status—The Answer in the Electrocardiogram

A woman in her late teens with a 1-year history of viral cardiomyopathy presented with decompensated heart failure. The patient’s echocardiogram was notable for a left ventricular ejection fraction of 20% to 25%. Physical examination was notable for bibasilar crackles on lung auscultation and lower-extremity edema. The patient was started on intravenous (IV) diuretic therapy, an IV milrinone infusion, and IV calcium therapy (as adjuvant therapy for ionotropic support; unknown dose). Over the next 5 days, she improved clinically and passed 7 liters of urine. On hospital days 6 and 7, she became increasingly somnolent with urinary incontinence, constipation, and decreased gait stability. Obstructive sleep apnea was believed to be the cause of her symptoms at that time, but she failed to improve with bilevel positive pressure ventilation and was transferred for further management. On arrival, she appeared euvolemic and had no focal neurologic deficits on examination but was somnolent (Richmond Agitation-Sedation Scale, −3). An electrocardiogram (ECG) was obtained (Figure 1). Question: What diagnosis should be considered?
Segmentation Guided Robust Multimodal Image Registration Using Local Correlation

This paper presents a unified variational framework for seamlessly integrating prior segmentation information into non-rigid registration procedures. Under this framework, in addition to the forces arises from the similarity measure in seeking for detailed correspondence, another set of forces generated by the prior segmentation contours can provide an extra guidance in assisting the alignment process towards a more meaningful, stable and noise-tolerant procedure. Local correlation (LC) is being used as the underlying similarity measures to handle intensity variations. We present several 2D/3D examples on synthetic and real data
Disparity estimation for the intermediate view interpolation of stereoscopic images

The paper presents a disparity estimation method that combines a phase-based disparity estimation algorithm with an energy-based variational refinement approach, and adapts the method for the application of intermediate view interpolation. The Gabor transform is implemented using a set of quadrature-pair filters for finding the local phase information as well as for estimating the correspondences in stereo pairs. Then the estimated coarse disparity is applied to the variational refinement process which involves solving a partial differential equation (PDE) associated with an edge-preserving regularization functional. Two stereo image pairs in which the original intermediate images are available were used to test the algorithm, where our interpolated intermediate images could be compared with the originals. The performance with PSNR results shows that our method can provide very good images without introducing obvious artifacts.
Safening grain sorghum injury from metsulfuron with growth regulator herbicides

Abstract Field and greenhouse experiments were conducted to evaluate the efficacy and safening of metsulfuron applied with dicamba, 2,4-D, clopyralid, and fluroxypyr with and without nonionic surfactant. Greenhouse data showed that 2,4-D and dicamba, but not fluroxypyr, safened grain sorghum from metsulfuron injury. In the field study, grain sorghum injury from metsulfuron was decreased when tank mixed with 2,4-D or dicamba but not when tank mixed with clopyralid or fluroxypyr. Tank mixes of 2,4-D or dicamba with metsulfuron did not reduce ivyleaf morningglory or velvetleaf control. At 4 wk after treatment (WAT), ivyleaf morningglory was controlled 95, 84, 59, and 91%, and velvetleaf was controlled 88, 82, 78, and 95% when metsulfuron was tank mixed with 2,4-D, dicamba, clopyralid, and fluroxypyr, respectively. In a separate field study, differential grain sorghum hybrid responses to a tank mix of metsulfuron + 2,4-D was examined. In general, a tank mix of metsulfuron and 2,4-D caused visible injury to al...
Evidence for the Influence of Surface Heat Fluxes on Turbulent Mixing of Microplastic Marine Debris

AbstractBuoyant microplastic marine debris (MPMD) is a pollutant in the ocean surface boundary layer (OSBL) that is submerged by wave-driven turbulent transport processes. This study analyzes observed MPMD surface concentrations in the Atlantic and Pacific Oceans to reveal a significant increase in concentrations during surface heating and a decrease during surface cooling. Turbulence-resolving large-eddy simulations of the OSBL for an idealized diurnal heating cycle suggest that turbulent downward fluxes of buoyant tracers are enhanced at night, facilitating deep submergence of plastics, and suppressed in heating conditions, resulting in surface-trapped MPMD. Simulations agree better with observations if enhanced mixing due to wave-driven Langmuir turbulence (LT) is included. The simulated time-dependent OSBL response results in hysteresis effects so that surface concentrations depend also on the phase of the diurnal heating cycle. The results demonstrate the controlling influence of surface heat fluxes ...
SUMOylation and Ubiquitylation Circuitry Controls Pregnane X Receptor Biology in Hepatocytes

Several nuclear receptor (NR) superfamily members are known to be the molecular target of either the small ubiquitin-related modifier (SUMO) or ubiquitin-signaling pathways. However, little is currently known regarding how these two post-translational modifications interact to control NR biology. We show that SUMO and ubiquitin circuitry coordinately modifies the pregnane X receptor (PXR, NR1I2) to play a key role in regulating PXR protein stability, transactivation capacity, and transcriptional repression. The SUMOylation and ubiquitylation of PXR is increased in a ligand- and tumor necrosis factor alpha–dependent manner in hepatocytes. The SUMO-E3 ligase enzymes protein inhibitor of activated signal transducer and activator of transcription-1 (STAT1) STAT-1 (PIAS1) and protein inhibitor of activated STAT Y (PIASy) drive high levels of PXR SUMOylation. Expression of protein inhibitor of activated stat 1 selectively increases SUMO(3)ylation as well as PXR-mediated induction of cytochrome P450, family 3, subfamily A and the xenobiotic response. The PIASy-mediated SUMO(1)ylation imparts a transcriptionally repressive function by ameliorating interaction of PXR with coactivator protein peroxisome proliferator-activated receptor gamma coactivator-1-alpha. The SUMO modification of PXR is effectively antagonized by the SUMO protease sentrin protease (SENP) 2, whereas SENP3 and SENP6 proteases are highly active in the removal of SUMO2/3 chains. The PIASy-mediated SUMO(1)ylation of PXR inhibits ubiquitin-mediated degradation of this important liver-enriched NR by the 26S proteasome. Our data reveal a working model that delineates the interactive role that these two post-translational modifications play in reconciling PXR-mediated gene activation of the xenobiotic response versus transcriptional repression of the proinflammatory response in hepatocytes. Taken together, our data reveal that the SUMOylation and ubiquitylation of the PXR interface in a fundamental manner directs its biologic function in the liver in response to xenobiotic or inflammatory stress.
Using LSF features for speaker verification in noise

An automatic, text-independent speaker verification (SV) system is proposed using Line Spectral Frequency (LSF) features. The state-of-the-art Gaussian Mixture Model with Universal Background Model (GMM-UBM) framework is used for speaker modeling and verification. A score-level fusion based technique is employed in order to extract complementary information from static and dynamic LSF features and improve the noise-robustness of the SV system. In addition, the speaker-discriminative power of different speech zones such as vowels, non-vowels, and transitions are investigated. Rapidly varying transition regions of speech are found to be most speaker-discriminative in high SNR conditions. Steady, high-energy vowel regions are robust against noise and are most speaker-discriminative in low SNR conditions. We show that selectively utilizing features from a combination of transition and steady vowel zones further improves the performance of the score-level fusion based SV system under noisy conditions.
Natural Language Processing in Accounting, Auditing and Finance: A Synthesis of the Literature with a Roadmap for Future Research

Natural language processing NLP is a part of the artificial intelligence domain focused on communication between humans and computers. NLP attempts to address the inherent problem that while human communications are often ambiguous and imprecise, computers require unambiguous and precise messages to enable understanding. The accounting, auditing and finance domains frequently put forth textual documents intended to communicate a wide variety of messages, including, but not limited to, corporate financial performance, management's assessment of current and future firm performance, analysts' assessments of firm performance, domain standards and regulations as well as evidence of compliance with relevant standards and regulations. NLP applications have been used to mine these documents to obtain insights, make inferences and to create additional methodologies and artefacts to advance knowledge in accounting, auditing and finance. This paper synthesizes the extant literature in NLP in accounting, auditing and finance to establish the state of current knowledge and to identify paths for future research. Copyright © 2016 John Wiley & Sons, Ltd.
Radial partition fluorescent immunoassay of thyrotropin. Analytic evaluation and clinical correlation.

The authors evaluated the analytic and clinical performance of a sensitive radial partition fluorescent enzyme immunoassay for thyrotropin (TSH) performed on StratusTM and compared it with a nonsensitive radioimmunoassay (RIA) method. Sensitivity of 0.15 mlU/L was obtained, and precision, specificity, and linearity were acceptable. A good correlation was observed between the two assays in samples from 311 hospitalized patients (r = 0.976). Stratus TSH results were outside the reference range for 20% of clinically euthyroid patients (n = 126), and 2.4% had undetectable levels. The clinically hyperthyroid group (n = 11) with the exception of one patient had TSH values below 0.2 mlU/L. Only 39% of hypothyroid patients on thyroid hormone replacement (n = 74) had TSH values in the reference range, with 38% and 23% exhibiting low and high values, respectively. All untreated primary hypothyroid patients (n = 8) had elevated TSH concentrations. The authors conclude that this sensitive TSH assay is useful for diagnosing hyperthyroidism when there is a clinical suspicion but cannot be recommended for thyroid screening in hospitalized patients.
Effect of chlorpromazine on antidiuretic response to noxious stimuli.

SummaryAdministration of chlorpromazine inhibits the antidiuretic response of rats to painful stimuli but has no significant effect on antidiuretic response to injection of either histamine or nicotine.
Abdominal pregnancy on the bladder wall following embryo transfer with cryopreserved-thawed embryos: a case report

Objective To describe the occurrence and management of an abdominal pregnancy of the bladder after ET with cryopreserved-thawed embryos. Design Case report. Setting Infertility program in a tertiary care hospital. Patient(s) A woman with secondary infertility and a history of breast cancer. Intervention(s) Transfer of cryopreserved-thawed embryos was performed, serial serum hormonal measurements were obtained, methotrexate was given IM, operative laparoscopy was performed. Main Outcome Measure(s) Documentation of abdominal pregnancy after transfer of cryopreserved-thawed embryos and its successful laparoscopic management. Result(s) Abdominal pregnancy occurred after ET of cryopreserved embryos in a patient with mild tubal disease. Diagnosis and management using laparoscopy were achieved. Conclusion(s) Abdominal pregnancy can occur using ET of cryopreserved-thawed embryos in a patient with mild tubal disease. If anatomically accessible, such a pregnancy can be managed successfully laparoscopically.
Subtotal penetrating keratoplasty for treating severe infectious corneal ulcer

Objective To evaluate the clinical therapeutic effect of subtotal penetrating keratoplasty for treating severe infectious corneal ulcer ,using glycerin or anhydrous chloridize calcium preservative cornea.Methods For 3 cases with bacterial corneal ulcer for whom drug treatment was useless,the rang of the corneal perforation and melting reached 8.0～8.5mm;For 5 cases with fungal corneal ulcer,the rang of the corneal infiltration 7.5mm,the depth reached full-thickness cornea, the corneal little perforation for 2 cases, hypopyon for 3 cases, subtotal penetrating keratoplasty have been performed.Results Seven cases were cured,5 cases of the corneal graft remained translucence,the corneal neovascular were formed in 2 cases.One eye was enucleated due to recurrent corneal inflammation.Conclusions Subtotal penetrating keratoplasty is an effective method for treating severe infectious corneal ulcer with glycerin or anhydrous chloridize calcium preservative cornea being used when lacking the fresh corneal materials.
248 ETHNIC DIFFERENCES IN CYTOKINES EXIST IN RECENT-ONSET SYSTEMIC LUPUS ERYTHEMATOSUS.

Purpose Systemic lupus erythematosus (SLE) is an autoimmune disease of unknown etiology that affects young black women more severely than white women. Cytokines are a crucial factor in initiating, maintaining, and subsequently down-modulating the immune response in autoimmune disease. Significant ethnic differences in cytokines have not been reported. We investigated ethnic differences in TH1, TH2, and inflammatory cytokines in black and white women with recent-onset SLE. Methods Healthy premenopausal women with SLE for less than 5 years were enrolled. A standardized disease activity measure (Systemic Lupus Activity Measure or SLAM) was performed, and a blood sample was taken to measure cytokine levels by ELISA. We measured the inflammatory cytokines IL-1b, IL-6, and TNFa; the TH1 cytokines IL-2 and IFNg; and the TH2 and anti-inflammatory cytokine IL-10. BD Biosciences assays were used, had less than a 15% inter- and intra-assay variability in our hands, and recovered 90-105% of spiked cytokine. Results Thirty-three black and 14 white women were enrolled. The black women were slightly younger (31.6 vs 38.8 yr, p > .05) but clinical disease was similar. ACR criteria, SLAM score, and patient and MD global assessment were similar. TNF was not different between black and white women. Higher levels of IFNg (25.7 6 22.4 vs 18.3 6 18), IL-1 (31.2 6 44.1 vs 18.6 6 38.9), IL-2 (45.1 6 92.8 vs 12.1 6 9.5), and IL-6 (27.8 6 61.6 vs 10.2 6 10.6) were present in black than white women, respectively, but was not significant (p > .05). IL-10 was significantly lower in black (10.7 6 18.6) compared to white (29.8 6 25.4, p = .001) women. Conclusion The propensity of young black females to earlier onset and more severe SLE may be due in part to the inadequate anti-inflammatory TH2 cytokine IL-10 in the presence of an enhanced inflammatory and TH1 cytokine profile.
Follicular atresia associated with concurrent initiation of gonadotropin-releasing hormone agonist and follicle-stimulating hormone for oocyte recruitment

The ability of gonadotropin-releasing hormone agonist (GnRHa) to cause an initial stimulation of serum gonadotropins was used for follicular recruitment for in vitro fertilization (IVF) in 12 patients with a history of low estradiol (E2) response to conventional gonadotropin stimulation. Stimulation was initiated on cycle day 3 with concurrent administration of leuprolide (1 mg/day subcutaneously) and follicle stimulating hormone (FSH, 4 ampules/day intramuscularly). An 8-fold increase in basal serum luteinizing hormone (LH) and a 4-fold increase in basal serum FSH was seen on cycle day 4. Serum progesterone levels rose significantly by day 6. When compared to prior IVF attempts in these patients, the mean day of human chorionic gonadotropin administration and corresponding E2 levels were not significantly different. More atretic oocytes and fewer preovulatory oocytes were retrieved using GnRHa, and no increase was seen in total oocytes retrieved. One patient was canceled for poor E2 response, and one patient conceived, with a current viable pregnancy. It is concluded that concurrent initiation of leuprolide and FSH stimulation on cycle day 3 in patients with prior low response does not improve oocyte recruitment, and the high LH environment generated from initial stimulation of the agonist may be detrimental to normal oocyte development.
Reduction of Core Binding Factor beta (CBFβ) Dosage Blocks T Cell Development.

Core binding factors (CBFs) are heterodimers consisting of a DNA binding subunit (Runx1, Runx2, or Runx3) and a non-DNA binding CBFβ subunit. CBFβ increases the affinity of the Runx subunits for DNA. Embryos deficient for Runx1 or CBFβ die at midgestation with a complete failure of definitive hematopoiesis due to a block in hematopoietic stem cell (HSC) emergence. To examine the role of core binding factors at later stages of hematopoiesis, we generated a hypomorphic Cbfb allele ( Cbfb rss ), that when carried over a Cbfb null allele ( Cbfb rss/− ) results in a 3-4 fold reduction in CBFβ protein levels. Although HSCs emerge in Cbfb rss/− animals, fetal T cell development is severely impaired. Here we examined the T cell developmental block in more detail by culturing fetal liver cells from Cbfb rss/− animals on OP9 stromal cells that express the Notch ligand Delta-like-1 (DL1) (Schmitt and Zuniga-Pflucker, Immunity17: 749, 2002). Fetal livers (E14.5) from Cbfb rss/− animals contained normal numbers of both c-kit+Sca-1+lin- cells and c-kit+IL7r+ lymphoid progenitors. Lin- fetal liver progenitors cultured on OP9-DL1 cells in the presence of IL-7 and Flt3L displayed a growth disadvantage relative to wild type cells, and a block at the double negative 1 (DN1, CD44+ CD25−) stage of T cell development. The T cell defect could be rescued by retroviral transduction of the CBFβ heterodimerization domain into lin- fetal liver cells, but not by a G61A/N104A mutant that cannot bind the Runx subunits. Genes whose expression was decreased in DN1 cells purified from the OP9-DL1 cultures included CD3 and the early T cell transcription factors GATA3 and TCF. Although expression of several Notch pathway genes (Notch1, Hes-1/5, Deltex-1) was mildly decreased, Notch signals were clearly transduced, suggesting that Notch signaling was intact. These data demonstrate that reduced CBFβ levels impair the differentiation of stem cells/progenitors into T cells at the earliest stage of T cell development. This in vitro model will be useful for characterizing the molecular circuitry involving CBFβ in T cell development, and for identifying CBFβ protein partners.
Community Theories of Change: Linking Environmental Justice to Sustainability through Stakeholder Perceptions in Milwaukee (WI, USA)

Environmental justice and sustainability are compatible lenses, yet action toward equity is often missing from urban sustainability initiatives. This study aims to assess the cohesion of these frameworks in practice. To do this, we parse individuals' theories of change, or how they identify and propose to resolve environmental injustices in the pursuit of sustainability. We posit that these theories of change are comprised of three main components: (1) perceived environmental benefits and burdens; (2) the causal pathways of environmental and social injustice; and (3) visions for positive change. Drawing from 35 stakeholder interviews in Milwaukee (WI, USA) we examine individual and institutional perspectives on environmental and social change and their links to the production of injustice. Our findings reveal that participants do not distinguish between environmental and social injustices. Instead, both social and environmental factors are implicated in injustice. Furthermore, we identify two mental maps for how social and economic change reproduce injustice. These findings suggest the need to reorient how urban injustice is considered and make efforts to acknowledge how a diversity of operational theories of change could either be divisive or could bring environmental justice and sustainability initiatives together.
Perspectives of DIG FinFETs for efficient terahertz detection applications

Dual-independent-gate (DIG) silicon FinFETs were recently shown capable of operating with ultra-steep subthreshold slope of 3.4 mV/dec at room-temperature due to a weak impact ionization induced positive feedback. In this work we discuss the perspectives of these devices for room-temperature terahertz detector applications. Our analysis shows that DIG-FinFETs can enable room-temperature current-responsivities up to two orders of magnitude larger than those of regular FET and Schottky diode detectors at room-temperature. The device operation, detector configurations, and the sources of noise in the device are discussed and rigorously analyzed; moreover the device is also benchmarked against other present-day direct detector technologies.
Some new results on the asymptotic analysis for diversity receivers

This article derives a new class of closed-form asymptotic expressions for computing the average symbol error rate (ASER) and outage probability/capacity performance measures of digital communications with diversity transceivers. Specifically, we study the efficacy of our recently proposed normalized asymptotic probability density function (PDF) of signal-to-noise ratio (SNR) method to both unify and simplify the analyses of selection diversity combining (SDC), maximal ratio combining (MRC) and equal gain combining (EGC) diversity techniques in different multipath fading environments and modulation schemes. Our approach requires only the knowledge of the first non-zero term of Poincare/Taylor series expansion of the PDF of diversity combiner output SNR (thereby circumventing the difficulties involved in computing coefficients of higher order approximations) while yielding significantly better predictions than the traditional high-SNR approximation, especially in the low and medium mean SNR regions.
Synthesis and reactivity of tantalum corrole complexes.

Reaction of the free base corrole (Mes2(p-OMePh)corrole)H3 with tantalum trialkyl precursors TaMe3Cl2 and TaBn3NtBu resulted in the formation of the tantalum dichloride (1) and tantalum imido (4) corrole complexes via alkane elimination. The X-ray crystal structures of these two compounds have been determined and the structural parameters are discussed. The Ta centre of 1 was found to sit out of the plane of the corrole ring by 0.903 A and is cis-ligated, similarly to what has been reported for group 4 porphyrin complexes. From complex 1 we synthesized the dimethyl derivative (2), the reactivity of which is compared to an analogous tantalum dimethyl porphyrin cation. The imido complex 4 reacted with triphenylmethanol and 4-methylbenzyl alcohol, resulting in different extents of protonation of the imido group.
Mental Health Correlates of Financial Mistreatment in the National Elder Mistreatment Study Wave II.

Objective: Whereas prevalence of elder financial mistreatment has received increased attention over the past decade, health and mental health correlates are rarely studied. Thus, the potential rele...
Batch Effect Removal via Batch-Free Encoding

Biological measurements often contain systematic errors, also known as "batch effects", which may invalidate downstream analysis when not handled correctly. The problem of removing batch effects is of major importance in the biological community. Despite recent advances in this direction via deep learning techniques, most current methods may not fully preserve the true biological patterns the data contains. In this work we propose a deep learning approach for batch effect removal. The crux of our approach is learning a batch-free encoding of the data, representing its intrinsic biological properties, but not batch effects. In addition, we also encode the systematic factors through a decoding mechanism and require accurate reconstruction of the data. Altogether, this allows us to fully preserve the true biological patterns represented in the data. Experimental results are reported on data obtained from two high throughput technologies, mass cytometry and single-cell RNA-seq. Beyond good performance on training data, we also observe that our system performs well on test data obtained from new patients, which was not available at training time. Our method is easy to handle, a publicly available code can be found at https://github.com/ushaham/BatchEffectRemoval2018.
Elimination of Age-Associated Hepatic Steatosis and Correction of Aging Phenotype by Inhibition of cdk4-C/EBPα-p300 Axis.

Summary The aging liver is affected by several disorders, including steatosis, that can lead to a decline of liver functions. Here, we present evidence that the cdk4-C/EBPα-p300 axis is a critical regulator of age-associated disorders, including steatosis. We found that patients with non-alcoholic fatty liver disease (NAFLD) have increased levels of cdk4 and that cdk4-resistant C/EBPα-S193A mice do not develop hepatic steatosis with advancing age. Underlying mechanisms include a block in C/EBPα activation and subsequent failure in activation of enzymes involved in the development of NAFLD. Inhibition of cdk4 in aged wild-type (WT) mice by a specific cdk4 inhibitor, PD-0332991, reduces C/EBPα-p300 complexes and eliminates hepatic steatosis. Moreover, the inhibition of cdk4 in aged mice reverses many age-related disorders. Mechanisms of correction include elimination of cellular senescence and alterations in the chromatin structure of hepatocytes. Thus, the inhibition of cdk4 might be considered as a therapeutic approach to correct age-associated liver disorders.
Distributed Detection with Unreliable Data Sources

In this chapter, we discuss networked detection problems for several practical network architectures such as parallel, multi-hop, and fully autonomous ad hoc networks. Following the taxonomy presented earlier, fundamental limits of networked inference in the presence of Byzantine attacks are first presented. Next, design of optimal countermeasures using the insights provided by the fundamental limits is discussed from a network designer’s perspective.
Demand Shaping Through Bundling and Product Configuration: A Dynamic Multiproduct Inventory-Pricing Model

In today’s digital age, with the aid of the internet and data mining, many firms use vertically differentiated product bundling to influence demand to match up with inventory status, especially in industries with short product life cycles. Despite this practice, there is little understanding on how exactly the inventory dynamics impact the bundling strategy, and, in turn, how the bundling strategy affects the firm's inventory decisions. To fill this gap, we present a dynamic model to analyze the optimal joint replenishment, pricing, and bundling decisions over time. A key enabler of our analysis is a novel demand model that transfers the discrete bundling decision and the corresponding pricing decision into a continuous market share decision. We show that the optimal policy is dictated by a no-order set in each period. For items in this set, we do not place replenishment orders, because these items are overstocked. The rest of the policy parameters -- the order-up-to-levels for the items that we do order, the bundling and pricing decisions, and the bundle assembly quantity -- all depend on the overstock levels. We also characterize how the optimal bundling decision depends on item complementarity, cost structure, inventory levels, demand uncertainty, and supply responsiveness.
Anticoagulant-Related Nephropathy in Kidney Biopsy: A Single-Center Report of 41 Cases

Rationale & Objective In 2009, the first case of acute kidney injury and occlusive red blood cell (RBC) tubular casts associated with a high international normalized ratio in a patient receiving warfarin was identified. This entity, named warfarin-related nephropathy, was later renamed anticoagulant-related nephropathy (ARN) after similar cases with other anticoagulants were described. We provide our 10-year experience with ARN based on a single-center kidney biopsy laboratory. Study Design The kidney pathology database at the Ohio State University Wexner Medical Center (OSUWMC) was searched for native kidney biopsy cases consistent with ARN. Clinical data were obtained from patient medical records. Setting & Participants Native kidney biopsies evaluated between January 1, 2009, and December 31, 2017 at OSUWMC. Results Among 8,636 native kidney biopsies reviewed at the OSUWMC, there were 41 (0.5%) patients for whom deterioration in kidney function could not be explained by kidney biopsy findings alone if anticoagulation was not considered. There were 63% men and 95% were white; average age was 62±14 years. Most were on warfarin therapy (N=28), although cases were also attributed to direct-acting anticoagulants (N=2), antiplatelet medications (N=1), heparin or enoxaparin (N=4), and disseminated intravascular coagulopathy (N=6). Morphologically, there was acute tubular necrosis and RBC casts. The majority of biopsies had an underlying glomerular disease and many patients had positive serologic test results. In all these cases, the severity of kidney failure, RBC tubular casts, and hematuria were disproportionate to glomerular morphologic changes. Limitations Selection bias in the decision to perform a kidney biopsy. Conclusions ARN is an uncommon diagnosis in kidney pathology practice, but it should be considered when the number of RBC tubular casts is disproportionate to the severity of glomerular changes in a kidney biopsy in patients either receiving anticoagulation therapy or who presented with acute coagulopathy. Our data suggest that anticoagulation aggravates underlying glomerular diseases rather than directly affecting the glomerular filtration barrier.
Apolipoprotein E/Amyloid-β Complex Accumulates in Alzheimer Disease Cortical Synapses via Apolipoprotein E Receptors and Is Enhanced by APOE4.

Apolipoprotein E (apoE) colocalizes with amyloid-β (Aβ) in Alzheimer disease (AD) plaques and in synapses, and evidence suggests that direct interactions between apoE and Aβ are important for apoE's effects in AD. The present work examines the hypothesis that apoE receptors mediate uptake of apoE/Aβ complex into synaptic terminals. Western blot analysis shows multiple SDS-stable assemblies in synaptosomes from human AD cortex; apoE/Aβ complex was markedly increased in AD compared with aged control samples. Complex formation between apoE and Aβ was confirmed by coimmunoprecipitation experiments. The apoE receptors low-density lipoprotein receptor (LDLR) and LDLR-related protein 1 (LRP1) were quantified in synaptosomes using flow cytometry, revealing up-regulation of LRP1 in early- and late-stage AD. Dual-labeling flow cytometry analysis of LRP1- and LDLR positives indicate most (approximately 65%) of LDLR and LRP1 is associated with postsynaptic density-95 (PSD-95)–positive synaptosomes, indicating that remaining LRP1 and LDLR receptors are exclusively presynaptic. Flow cytometry analysis of Nile red labeling revealed a reduction in cholesterol esters in AD synaptosomes. Dual-labeling experiments showed apoE and Aβ concentration into LDLR and LRP1-positive synaptosomes, along with free and esterified cholesterol. Synaptic Aβ was increased by apoE4 in control and AD samples. These results are consistent with uptake of apoE/Aβ complex and associated lipids into synaptic terminals, with subsequent Aβ clearance in control synapses and accumulation in AD synapses.
Perspectives on Data Analysis in Metabolomics: Points of Agreement and Disagreement from the 2018 ASMS Fall Workshop

In November 2018, the American Society for Mass Spectrometry hosted the Annual Fall Workshop on informatic methods in metabolomics. The Workshop included sixteen lectures presented by twelve invited speakers. The focus of the talks was untargeted metabolomics performed with liquid chromatography/mass spectrometry. In this review, we highlight five recurring topics that were covered by multiple presenters: (i) data sharing, (ii) artifacts and contaminants, (iii) feature degeneracy, (iv) database organization, and (v) requirements for metabolite identification. Our objective here is to present viewpoints that were widely shared among participants, as well as those in which varying opinions were articulated. We note that most of the presenting speakers employed different data processing software, which underscores the diversity of informatic programs currently being used in metabolomics. We conclude with our thoughts on the potential role of reference datasets as a step towards standardizing data processing methods in metabolomics.
Electric vehicles and residential parking in an urban environment: Results from a stated preference experiment

Abstract This paper presents the results of a preference survey of 1545 respondents’ willingness to purchase electric vehicles (EVs) in Philadelphia. We pay particular attention to respondents’ willingness to pay for convenient charging systems and parking spaces. If the value of dedicated parking substantially outweighs the value of convenient charging systems, residential-based on-street charging systems are unlikely to ever be politically palatable. As expected, respondents are generally willing to pay for longer range, shorter charging times, lower operating costs, and shorter parking search times. For a typical respondent, a $100 per month parking charge decreases the odds of purchasing an EV by around 65%. Across mixed logit and latent class models, we find substantial variation in the willingness to pay for EV range, charge time, and ease of parking. Of note, we find two primary classes of respondents with substantially different EV preferences. The first class tends to live in multifamily housing units in central parts of the city and puts a high value on parking search time and the availability of on-street charging stations. The second class, whose members are likelier to be married, wealthy, conservative, and residing in single-family homes in more distant neighborhoods, are willing to pay more for EV range and charge time, but less for parking than the first group. They are also much likelier to consider purchasing EVs at all. We recommend that future research into EV adoption incorporate neighborhood-level features, like parking availability and average trip distances, which vary by neighborhood and almost certainly influence EV adoption.
Distribution of agitation and related symptoms among hospitalized patients using a scalable natural language processing method.

Abstract Background Agitation is a common feature of many neuropsychiatric disorders. Objective Understanding the prevalence, implications, and characteristics of agitation among hospitalized populations can facilitate more precise recognition of disability arising from neuropsychiatric diseases. Methods We developed two agitation phenotypes using an expansion of expert curated term lists. These phenotypes were used to characterize five years of psychiatric admissions. The relationship of agitation symptoms and length of stay was examined. Results Among 4548 psychiatric admissions, 1134 (24.9%) included documentation of agitation based on the primary agitation phenotype. These symptoms were greater among individuals with public insurance, and those with mania and psychosis compared to major depressive disorder. Greater symptoms were associated with longer hospital stay, with ~0.9 day increase in stay for every 10% increase in agitation phenotype. Conclusion Agitation was common at hospital admission and associated with diagnosis and longer length of stay. Characterizing agitation-related symptoms through natural language processing may provide new tools for understanding agitated behaviors and their relationship to delirium.
TATTER: A hypothesis testing tool for multi-dimensional data

Abstract The two-sample hypothesis test quantifies whether distributions p and q are different, given the corresponding finite samples drawn from each. This problem appears in a legion of applications in astronomy, ranging from data mining to data analysis and inference. For decades, the Kolmogorov–Smirnov test has been astronomers’ first choice to answer this question, but it has a major drawback, a generalization to multi-dimensional data sets is not straightforward. To fill this gap, we present a nonparametric estimator for comparing given multi-dimensional distributions drawn from them. This method employs a kernel function to construct an unbiased estimator of the Maximum Mean Discrepancy (MMD) distance between the two distributions that generated the observed data. We perform controlled numerical experiments in Gaussian, non-Gaussian, and multi-dimensional finite sample settings and test the performance of MMD estimator in each experiment. We then discuss some of the applications of this method in astronomy data analysis.
MCS+: An Efficient Algorithm for Crawling the Community Structure in Multiplex Networks

In this article, we consider the problem of crawling a multiplex network to identify the community structure of a layer-of-interest. A multiplex network is one where there are multiple types of relationships between the nodes. In many multiplex networks, some layers might be easier to explore (in terms of time, money etc.). We propose MCS+, an algorithm that can use the information from the easier to explore layers to help in the exploration of a layer-of-interest that is expensive to explore. We consider the goal of exploration to be generating a sample that is representative of the communities in the complete layer-of-interest. This work has practical applications in areas such as exploration of dark (e.g., criminal) networks, online social networks, biological networks, and so on. For example, in a terrorist network, relationships such as phone records, e-mail records, and so on are easier to collect; in contrast, data on the face-to-face communications are much harder to collect, but also potentially more valuable. We perform extensive experimental evaluations on real-world networks, and we observe that MCS+ consistently outperforms the best baseline—the similarity of the sample that MCS+ generates to the real network is up to three times that of the best baseline in some networks. We also perform theoretical and experimental evaluations on the scalability of MCS+ to network properties, and find that it scales well with the budget, number of layers in the multiplex network, and the average degree in the original network.
Capturing the quotidian: casta paintings and demographic trends in late colonial Mexico

In 1581, Spanish magistrates near Celaya investigated the murder of Andres Vasquez at the hands of his employer, the infamous Antonio de Espejo.1 While the case itself centered on the dispute that ...
Assessing the Potential of Crowd-Shipping for Food Rescue Logistics Using Agent-Based Modeling

Food insecurity in the U.S. is a national concern. More than 30% of available food supply at the retail and consumer level in the U.S. is wasted each year and sent to landfills. This wholesome food could help address food insecurity problem by feeding the hungry families. Restaurants are a major source of food waste in the U.S. However, less than 5% of the more than 1 million restaurants in the U.S. currently donate food to the hungry. One of the biggest barriers to food donation from restaurants is transportation. Crowd-sourced transportation, known as “crowd-shipping,” is a potential solution, in which individual volunteers use their personal vehicles to collect donated surplus food from restaurants and deliver it to food-insecure recipients. However, viability and effectiveness of such a program require that the number of participating restaurants and crowd-shippers are appropriately balanced and grow over time. This paper describes a conceptual agent-based model that was developed to examine the impact of initial restaurants and crowd-shipper participation levels on the number of meals delivered to food-insecure people over time. Preliminary experimental results demonstrate that increasing the initial participation levels does not necessarily lead to a uniformly better system performance over time—maintaining the right ratio of crowd-shippers to restaurants is critical to success.
And a Letter

Three months and a day ago I started the first typing of this — this work, this book, I embarked on this voyage, this venture, and I’ve just finished reading the seventh meeting of the York seminar: I cannot, or should not excerpt it but bring it whole; if I remove unfinished sentences, the opacity, and the repetitions, it will be as tightly colored a mosaic, as sharply articulated a crystallery (if I may say so) as I said of the 1964–65 tutorial. I thus would have to go over the 48 pages of the transcript (one of the longer ones) and do the removing I just mentioned to make it shine (shine forth). Then I would have to have a photocopy made (because I am making two copies of the whole manuscript of this enterprise), and this would be too heavy to take along home: we’re leaving in a week. Thus I have accepted the appropriateness of interruption until I can take up the task again at home, although I don’t know yet quite how soon that will be possible, what the circumstances are. I’ll send the transcripts of the first five meetings home and take those of the remaining 11 — some 500 pages — with me for fear they might get lost. I am sad, of course, that I have not been able to finish this first draft during my semester off.
Female Rats Are More Sensitive to Enhanced Reinstatement of Alcohol Seeking Following Exposure to Both Alcohol-related Cues and Yohimbine

Exposure to cues previously associated with drug use and to stress can each promote craving and increase the risk of relapse. Preclinical studies that have combined these stimuli in tests of the re...
Effects of Starting Powder Characteristics on Bulk Assembly of Titania

Seven nanoscale titanias synthesized from a sulfate process were investigated for rheological characterization. Alteration of synthesis parameters had resulted in variation of the powder surface area and soluble sulfate level from powder to powder. The powder differences were further corroborated in stress-controlled rheometry where the viscoelastic yield stress of a suspension was seen to vary strongly with processing history. Capillary and torque rheometry further showed the dependence of processing history on steady-state extrusion pressure and steady-state mixing torque. The powders were washed to determine whether sulfate equilibration through washing could be used to circumvent the synthesis parameter differences.
An Internet Appendix to: The Impact of Duplicate Orders on Demand Estimation and Capacity Investment

Motivated by a $2.2 billion inventory write-off by Cisco Systems, we investigate how duplicate orders can lead a manufacturer to err in estimating the demand rate and customers' sensitivity to delay, and to make faulty decisions about capacity investment. We consider a manufacturer that sells through two distributors. If a customer finds that his distributor is out-of-stock, then he will sometimes seek to make a purchase from the other distributor; if the latter is also out-of-stock, the customer will order from both distributors. When his order is filled by one of the distributors, the customer cancels any duplicate orders. Furthermore, the customer cancels all of his outstanding orders after a random period of time. Assuming that the manufacturer is unaware of duplicate orders, we prove that she will overestimate both the demand rate and the cancellation rate. Surprisingly, failure to account for duplicate orders can cause short-term underinvestment in capacity. However, in long term equilibrium under stable demand conditions the manufacturer overinvests in capacity. Our results suggest that Cisco's write-off was caused by estimation errors and cannot be blamed entirely on the economic downturn. Finally, we provide some guidance on estimation in the presence of double orders. The majority of the results in our paper apply to the base case where the manufacturer dedicates a fixed fraction of her capacity to each distributor. This Appendix shows that the results remain true when the manufacturer fills distributors' orders FIFO from pooled capacity.