cssi/SciSciGPT-SciSciNet huggingface dataset:
Resonance with subthreshold oscillatory drive organizes activity and optimizes learning in neural networks.

Network oscillations across and within brain areas are critical for learning and performance of memory tasks. While a large amount of work has focused on the generation of neural oscillations, their effect on neuronal populations’ spiking activity and information encoding is less known. Here, we use computational modeling to demonstrate that a shift in resonance responses can interact with oscillating input to ensure that networks of neurons properly encode new information represented in external inputs to the weights of recurrent synaptic connections. Using a neuronal network model, we find that due to an input current-dependent shift in their resonance response, individual neurons in a network will arrange their phases of firing to represent varying strengths of their respective inputs. As networks encode information, neurons fire more synchronously, and this effect limits the extent to which further “learning” (in the form of changes in synaptic strength) can occur. We also demonstrate that sequential patterns of neuronal firing can be accurately stored in the network; these sequences are later reproduced without external input (in the context of subthreshold oscillations) in both the forward and reverse directions (as has been observed following learning in vivo). To test whether a similar mechanism could act in vivo, we show that periodic stimulation of hippocampal neurons coordinates network activity and functional connectivity in a frequency-dependent manner. We conclude that resonance with subthreshold oscillations provides a plausible network-level mechanism to accurately encode and retrieve information without overstrengthening connections between neurons.
Neuronal pentraxin 1: A synaptic-derived plasma biomarker in Alzheimer's disease.

Abstract Synaptic neurodegeneration is thought to be an early event initiated by soluble β-amyloid (Aβ) aggregates that closely correlates with cognitive decline in Alzheimer disease (AD). Apolipoprotein e4 (APOE4) is the most common genetic risk factor for both familial AD (FAD) and sporadic AD; it accelerates Aβ aggregation and selectively impairs glutamate receptor function and synaptic plasticity. However, its molecular mechanisms remain elusive and these synaptic deficits are difficult to monitor. AD- and APOE4-dependent plasma biomarkers have been proposed, but synapse-related plasma biomarkers are lacking. We evaluated neuronal pentraxin 1 (NP1), a potential CNS-derived plasma biomarker of excitatory synaptic pathology. NP1 is preferentially expressed in brain and involved in glutamate receptor internalization. NP1 is secreted presynaptically induced by Aβ oligomers, and implicated in excitatory synaptic and mitochondrial deficits. Levels of NP1 and its fragments were increased in a correlated fashion in both brain and plasma of 7–8 month-old E4FAD mice relative to E3FAD mice. NP1 was also found in exosome preparations and reduced by dietary DHA supplementation. Plasma NP1 was higher in E4FAD+ (APOE4+/+/FAD+/−) relative to E4FAD- (non-carrier; APOE4+/+/FAD−/−) mice, suggesting NP1 is modulated by Aβ expression. Finally, relative to normal elderly, plasma NP1 was also elevated in patients with mild cognitive impairment (MCI) and elevated further in the subset who progressed to early-stage AD. In those patients, there was a trend towards increased NP1 levels in APOE4 carriers relative to non-carriers. These findings indicate that NP1 may represent a potential synapse-derived plasma biomarker relevant to early alterations in excitatory synapses in MCI and early-stage AD.
Concave regression: value-constrained estimation and likelihood ratio-based inference

We propose a likelihood ratio statistic for forming hypothesis tests and confidence intervals for a nonparametrically estimated univariate regression function, based on the shape restriction of concavity (alternatively, convexity). Dealing with the likelihood ratio statistic requires studying an estimator satisfying a null hypothesis, that is, studying a concave least-squares estimator satisfying a further equality constraint. We study this null hypothesis least-squares estimator (NLSE) here, and use it to study our likelihood ratio statistic. The NLSE is the solution to a convex program, and we find a set of inequality and equality constraints that characterize the solution. We also study a corresponding limiting version of the convex program based on observing a Brownian motion with drift. The solution to the limit problem is a stochastic process. We study the optimality conditions for the solution to the limit problem and find that they match those we derived for the solution to the finite sample problem. This allows us to show the limit stochastic process yields the limit distribution of the (finite sample) NLSE. We conjecture that the likelihood ratio statistic is asymptotically pivotal, meaning that it has a limit distribution with no nuisance parameters to be estimated, which makes it a very effective tool for this difficult inference problem. We provide a partial proof of this conjecture, and we also provide simulation evidence strongly supporting this conjecture.
Joint Alignment from Pairwise Differences with a Noisy Oracle

In this work we consider the problem of recovering n discrete random variables \(x_i\in \{0,\ldots ,k-1\}, 1 \le i \le n\) with the smallest possible number of queries to a noisy oracle that returns for a given query pair \((x_i,x_j)\) a noisy measurement of their modulo k pairwise difference, i.e., \(y_{ij} = x_i-x_j \ (\mathrm {mod}\ k)\). This is a joint discrete alignment problem with important applications in computer vision [12, 23], graph mining [20], and spectroscopy imaging [22]. Our main result is a recovery algorithm (up to some offset) that solves with high probability the non-convex maximum likelihood estimation problem using \(O(n^{1+o(1)})\) queries.
In Vivo Calcium Imaging of Cardiomyocytes in the Beating Mouse Heart With Multiphoton Microscopy.

Background: Understanding the microscopic dynamics of the beating heart has been challenging due to the technical nature of imaging with micrometer resolution while the heart moves. The development of multiphoton microscopy has made in vivo, cell-resolved measurements of calcium dynamics and vascular function possible in motionless organs such as the brain. In heart, however, studies of in vivo interactions between cells and the native microenvironment are behind other organ systems. Our goal was to develop methods for intravital imaging of cardiac structural and calcium dynamics with microscopic resolution. Methods: Ventilated mice expressing GCaMP6f, a genetically-encoded calcium indicator, received a thoracotomy to provide optical access to the heart. Vasculature was labeled with an injection of dextran-labeled dye. The heart was partially stabilized by a titanium probe with a glass window. Images were acquired at 30 frames per second with spontaneous heartbeat and continuously-running, ventilated breathing. The data were reconstructed into three-dimensional volumes showing tissue structure, vasculature, and GCaMP6f signal in cardiomyocytes as a function of both the cardiac and respiratory cycle. Results: We demonstrated the capability to simultaneously measure calcium transients, vessel size, and tissue displacement in three dimensions with micrometer resolution. Reconstruction at various combinations of cardiac and respiratory phase enabled measurement of regional and single-cell cardiomyocyte calcium transients (GCaMP6f fluorescence). GCaMP6f fluorescence transients in individual, aberrantly-firing cardiomyocytes were also quantified. Comparisons of calcium dynamics (rise-time and tau) at varying positions within the ventricle wall showed no significant depth dependence. Conclusion: This method enables studies of coupling between contraction and excitation during physiological blood perfusion and breathing at high spatiotemporal resolution. These capabilities could lead to a new understanding of normal and disease function of cardiac cells.
The secret downing street memo and the politics of truth: A performance text

Reading forward from the recently released secret Downing Street Memos, to the 2001 No Child Left Behind Act, in this performance text I critique the Bush Administration and its reliance on science, or evidence-based models of inquiry (SBR). SBR raises issues concerning the politics of truth and evidence. These issues intersect with the ways in which a given political regime fixes facts to fit ideology. Three versions of SBR are discussed, as is a model of science as disruptive cultural practice. I conclude by calling for a merger of critical pedagogy with a prophetic, feminist post-pragmatism.
Learning Shape Priors for Single-View 3D Completion and Reconstruction

The problem of single-view 3D shape completion or reconstruction is challenging, because among the many possible shapes that explain an observation, most are implausible and do not correspond to natural objects. Recent research in the field has tackled this problem by exploiting the expressiveness of deep convolutional networks. In fact, there is another level of ambiguity that is often overlooked: among plausible shapes, there are still multiple shapes that fit the 2D image equally well; i.e., the ground truth shape is non-deterministic given a single-view input. Existing fully supervised approaches fail to address this issue, and often produce blurry mean shapes with smooth surfaces but no fine details. In this paper, we propose ShapeHD, pushing the limit of single-view shape completion and reconstruction by integrating deep generative models with adversarially learned shape priors. The learned priors serve as a regularizer, penalizing the model only if its output is unrealistic, not if it deviates from the ground truth. Our design thus overcomes both levels of ambiguity aforementioned. Experiments demonstrate that ShapeHD outperforms state of the art by a large margin in both shape completion and shape reconstruction on multiple real datasets.
DeepMasterPrints: Generating MasterPrints for Dictionary Attacks via Latent Variable Evolution *

Recent research has demonstrated the vulnerability of fingerprint recognition systems to dictionary attacks based on MasterPrints. MasterPrints are real or synthetic fingerprints that can fortuitously match with a large number of fingerprints thereby undermining the security afforded by fingerprint systems. Previous work by Roy et al. generated synthetic MasterPrints at the feature-level. In this work we generate complete image-level MasterPrints known as DeepMasterPrints, whose attack accuracy is found to be much superior than that of previous methods. The proposed method, referred to as Latent Variable Evolution, is based on training a Generative Adversarial Network on a set of real fingerprint images. Stochastic search in the form of the Covariance Matrix Adaptation Evolution Strategy is then used to search for latent input variables to the generator network that can maximize the number of impostor matches as assessed by a fingerprint recognizer. Experiments convey the efficacy of the proposed method in generating DeepMasterPrints. The underlying method is likely to have broad applications in fingerprint security as well as fingerprint synthesis.
Small molecules inhibit ex vivo tumor growth in bone.

Abstract Bone is a common site of metastasis for breast, prostate, lung, kidney and other cancers. Bone metastases are incurable, and substantially reduce patient quality of life. To date, there exists no small-molecule therapeutic agent that can reduce tumor burden in bone. This is partly attributed to the lack of suitable in vitro assays that are good models of tumor growth in bone. Here, we take advantage of a novel ex vivo model of bone colonization to report a series of pyrrolopyrazolone small molecules that inhibit cancer cell invasion and ex vivo tumor growth in bone at single-digit micromolar concentration. We find that the compounds modulated the expression levels of genes associated with bone-forming osteoblasts, bone-destroying osteoclasts, cancer cell viability and metastasis. Our compounds provide chemical tools to uncover novel targets and pathways associated with bone metastasis, as well as for the development of compounds to prevent and reverse bone tumor growth in vivo.
Oral thermosensing by murine trigeminal neurons: modulation by capsaicin, menthol and mustard oil.

Key points Orosensory thermal trigeminal afferent neurons respond to cool, warm, and nociceptive hot temperatures with the majority activated in the cool range. Many of these thermosensitive trigeminal orosensory afferent neurons also respond to capsaicin, menthol, and/or mustard oil (allyl isothiocyanate) at concentrations found in foods and spices. There is significant but incomplete overlap between afferent trigeminal neurons that respond to oral thermal stimulation and to the above chemesthetic compounds. Capsaicin sensitizes warm trigeminal thermoreceptors and orosensory nociceptors; menthol attenuates cool thermoresponses. Abstract When consumed with foods, mint, mustard, and chili peppers generate pronounced oral thermosensations. Here we recorded responses in mouse trigeminal ganglion neurons to investigate interactions between thermal sensing and the active ingredients of these plants - menthol, allyl isothiocyanate (AITC), and capsaicin, respectively - at concentrations found in foods and commercial hygiene products. We carried out in vivo confocal calcium imaging of trigeminal ganglia in which neurons express GCaMP3 or GCAMP6s and recorded their responses to oral stimulation with thermal and the above chemesthetic stimuli. In the V3 (oral sensory) region of the ganglion, thermoreceptive neurons accounted for ∼10% of imaged neurons. We categorized them into three distinct classes: cool-responsive and warm-responsive thermosensors, and nociceptors (responsive only to temperatures ≥43-45 °C). Menthol, AITC, and capsaicin also elicited robust calcium responses that differed markedly in their latencies and durations. Most of the neurons that responded to these chemesthetic stimuli were also thermosensitive. Capsaicin and AITC increased the numbers of warm-responding neurons and shifted the nociceptor threshold to lower temperatures. Menthol attenuated the responses in all classes of thermoreceptors. Our data show that while individual neurons may respond to a narrow temperature range (or even bimodally), taken collectively, the population is able to report on graded changes of temperature. Our findings also substantiate an explanation for the thermal sensations experienced when one consumes pungent spices or mint.
Distribution‐free estimation of local growth rates around interval censored anchoring events

Biological processes are usually defined on timelines that are anchored by specific events. For example, cancer growth is typically measured by the change in tumor size from the time of oncogenesis. In the absence of such anchoring events, longitudinal assessments of the outcome lose their temporal reference. In this paper, we considered the estimation of local change rates in the outcomes when the anchoring events are interval-censored. Viewing the subject-specific anchoring event times as random variables from an unspecified distribution, we proposed a distribution-free estimation method for the local growth rates around the unobserved anchoring events. We expressed the rate parameters as stochastic functionals of the anchoring time distribution and showed that under mild regularity conditions, consistent and asymptotically normal estimates of the rate parameters could be achieved, with a n convergence rate. We conducted a carefully designed simulation study to evaluate the finite sample performance of the method. To motivate and illustrate the use of the proposed method, we estimated the skeletal growth rates of male and female adolescents, before and after the unobserved pubertal growth spurt (PGS) times.
National Cancer Institute Centers and Society of Surgical Oncology Cancer Research Synergy.

Abstract Background The objective of this study was to examine the influence of Surgical Society Oncology (SSO) membership and National Cancer Institute (NCI) status on the academic output of surgical faculty. Methods NCI cancer program status for each department of surgery was identified with publically available data, whereas SSO membership was determined for every faculty member. Academic output measures such as NIH funding, publications, and citations were analyzed in subsets by the type of cancer center (NCI comprehensive cancer center [CCC]; NCI cancer center [NCICC]; and non-NCI center) and SSO membership status. Results Of the surgical faculty, 2537 surgeons (61.9%) were from CCC, whereas 854 (20.8%) were from NCICC. At the CCC, 22.7% of surgeons had a history of or current NIH funding, compared with 15.8% at the NCICC and 11.8% at the non-NCI centers. The academic output of SSO members was higher at NCICC (52 ± 113 publications/1266 ± 3830 citations) and CCC (53 ± 92/1295 ± 4001) compared with nonmembers (NCICC: 26 ± 78/437 ± 2109; CCC: 37 ± 91/670 ± 3260), respectively, P Conclusions CCCs have significantly higher academic output and NIH funding. Recruitment of SSO members, a focus on higher performing divisions, and NIH funding are factors that non-NCI cancer centers may be able to focus on to improve academic productivity to aid in obtaining NCI designation.
Which Source Possesses the Best Data on the Empirical Aspects of Criminal Events? A Theory of Opportunity and Necessary Conditions

Offenders and nonoffenders possess valuable information about crime. But which possesses the best data? This is a complex issue, so I narrow my focus to data on empirical aspects of criminal events...
Alfuzosin 10 mg once daily prevents overall clinical progression of benign prostatic hyperplasia but not acute urinary retention: results of a 2-year placebo-controlled study

OBJECTIVES To evaluate the effect of alfuzosin 10 mg once daily administered for 2 years on progression events in men with lower urinary tract symptoms/benign prostatic hyperplasia (LUTS/BPH). PATIENTS AND METHODS In all, 1522 men at risk of having progression events from LUTS/BPH were randomized to receive alfuzosin 10 mg once daily (759) or placebo (763) for 2 years. Endpoints assessed were the occurrence of a first episode of acute urinary retention (AUR; primary) and the need for BPH-related surgery. Post hoc analyses included a deterioration in the International Prostate Symptom Score (IPSS) of ≥ 4 points and overall clinical progression of BPH (occurrence of AUR and/or surgery and/or symptom deterioration). RESULTS Over 2 years, symptom deterioration was the most common progression event (14.3%), followed by BPH-related surgery (5.8%) and AUR (2.0%). Alfuzosin did not reduce the risk of AUR (alfuzosin 2.1% vs placebo 1.8%, P = 0.82) but tended to reduce the risk of surgery (5.1% vs 6.5%, P = 0.18); the reduction in risk (RR) and 95% confidence interval with alfuzosin was 22 (−18 to 48)%; and significantly reduced the risk of symptom deterioration (11.7% vs 16.8%; P = 0.0013); the RR was 30 (10–46)%. The overall clinical progression of BPH was significantly lower with alfuzosin than with placebo (16.3% vs 22.1%, P < 0.001); RR 26 (9–40)%. Alfuzosin also significantly improved the IPSS (P = 0.017), quality of life (P < 0.001) and peak flow rate (P = 0.001) compared with placebo. Baseline levels of prostate-specific antigen (PSA) predicted both AUR and BPH-related surgery events, while the baseline postvoid residual urine volume predicted symptom deterioration. The incidence of adverse events with alfuzosin was comparable to that with placebo. CONCLUSIONS Alfuzosin 10 mg once daily prevents the overall clinical progression of BPH, defined by the occurrence of a deterioration in IPSS of ≥ 4 points and/or AUR and/or BPH-related surgery, but does not reduce the primary occurrence of AUR. Alfuzosin significantly improves LUTS and quality of life over 2 years, and is well tolerated.
Logistic Regression, Conditional†

This section describes the conditional logistic regression model. This model is appropriate when one wishes to model a binary outcome variable with matched or highly stratified data and when one is not interested in matched sets or stratum effects. The resulting fitted model may be used to estimate odds ratios in the same manner as is done with the usual logistic regression model. Examples of estimation and interpretation are given. Keywords: odds ratios; matched analyses; stratified analyses; matched case–control studies; conditional inference
Failure of an Educational Intervention to Improve Consultation and Implications for Healthcare Consultation.

INTRODUCTION Consultation of another physician for his or her specialized expertise regarding a patient's care is a common occurrence in most physicians' daily practice, especially in the emergency department (ED). Therefore, the ability to communicate effectively with another physician during a patient consultation is an essential skill. However, there has been limited research on a standardized method for a physician to physician consultation with little guidance on teaching consultations to physicians in training. The objective of our study was to measure the effect of a structured consultation intervention on both content standardization and quality of medical student consultations. METHODS Senior medical students were assessed on a required emergency medicine rotation with a physician phone consultation during a standardized, simulated chest pain case. The intervention groups received a standard consult checklist as part of their orientation to the rotation, followed by a video recording of a good consult call and a bad consult call with commentary from an emergency physician. The intervention was given to students every other month, alternating with a control group who received no additional education. Recordings were reviewed by three second-year internal medicine residents pursuing a fellowship in cardiology. Each recording was evaluated by two of the three reviewers and scored using a standardized checklist. RESULTS Providing a standardized consultation intervention did not improve students' ability to communicate with consultants. In addition, there was variability between evaluators in regards to how they received the same information and how they perceived the quality of the same recorded consultation calls. Evaluator inter-rater reliability (IRR) was poor on the questions of 1) would you have any other questions of the student calling the consult and 2) did the student calling the consult provide an accurate account of information and case detail. The IRR was also poor on objective data such as whether the student stated their name. CONCLUSIONS A brief intervention may not be enough to change complex behavior such as a physician to physician consultant communication. Importantly, despite consultants listening to the same audio recordings, the information was processed differently. Future investigations should focus on both those delivering as well as those receiving a consultation.
A permutation-based Bayesian approach for inverse covariance estimation

Covariance estimation and selection for multivariate datasets in a high-dimensional regime is a fundamental problem in modern statistics. Gaussian graphical models are a popular class of models use...
Lasso ANOVA decompositions for matrix and tensor data

Abstract Consider the problem of estimating the entries of an unknown mean matrix or tensor given a single noisy realization. In the matrix case, this problem can be addressed by decomposing the mean matrix into a component that is additive in the rows and columns, i.e. the additive ANOVA decomposition of the mean matrix, plus a matrix of elementwise effects, and assuming that the elementwise effects may be sparse. Accordingly, the mean matrix can be estimated by solving a penalized regression problem, applying a lasso penalty to the elementwise effects. Although solving this penalized regression problem is straightforward, specifying appropriate values of the penalty parameters is not. Leveraging the posterior mode interpretation of the penalized regression problem, moment-based empirical Bayes estimators of the penalty parameters can be defined. Estimation of the mean matrix using these moment-based empirical Bayes estimators can be called LANOVA penalization, and the corresponding estimate of the mean matrix can be called the LANOVA estimate. The empirical Bayes estimators are shown to be consistent. Additionally, LANOVA penalization is extended to accommodate sparsity of row and column effects and to estimate an unknown mean tensor. The behavior of the LANOVA estimate is examined under misspecification of the distribution of the elementwise effects, and LANOVA penalization is applied to several datasets, including a matrix of microarray data, a three-way tensor of fMRI data and a three-way tensor of wheat infection data.
A Survey on Modality Characteristics, Performance Evaluation Metrics, and Security for Traditional and Wearable Biometric Systems

Biometric research is directed increasingly toward Wearable Biometric Systems (WBS) for user authentication and identification. However, prior to engaging in WBS research, how their operational dynamics and design considerations differ from those of Traditional Biometric Systems (TBS) must be understood. While the current literature is cognizant of those differences, there is no effective work that summarizes the factors where TBS and WBS differ, namely, their modality characteristics, performance, security, and privacy. To bridge the gap, this article accordingly reviews and compares the key characteristics of modalities, contrasts the metrics used to evaluate system performance, and highlights the divergence in critical vulnerabilities, attacks, and defenses for TBS and WBS. It further discusses how these factors affect the design considerations for WBS, the open challenges, and future directions of research in these areas. In doing so, the article provides a big-picture overview of the important avenues of challenges and potential solutions that researchers entering the field should be aware of. Hence, this survey aims to be a starting point for researchers in comprehending the fundamental differences between TBS and WBS before understanding the core challenges associated with WBS and its design.
Formational bounds of link prediction in collaboration networks

Link prediction in collaboration networks is often solved by identifying structural properties of existing nodes that are disconnected at one point in time, and that share a link later on. The maximally possible recall rate or upper bound of this approach’s success is capped by the proportion of links that are formed among existing nodes embedded in these properties. Consequentially, sustained links as well as links that involve one or two new network participants are typically not predicted. The purpose of this study is to highlight formational constraints that need to be considered to increase the practical value of link prediction methods targeted for collaboration networks. In this study, we identify the distribution of basic link formation types based on four large-scale, over-time collaboration networks, showing that roughly speaking, 25% of links represent continued collaborations, 25% of links are new collaborations between existing authors, and 50% are formed between an existing author and a new network member. This implies that for collaboration networks, increasing the accuracy of computational link prediction solutions may not be a reasonable goal when the ratio of collaboration links that are eligible to the classic link prediction process is low.
Arming in the global economy: The importance of trade with enemies and friends

ABSTRACT We analyze how trade openness matters for interstate conflict over productive resources. Our analysis features a terms-of-trade channel that makes security policies trade-regime dependent. Specifically, trade between two adversaries reduces each one's incentive to arm given the opponent's arming. If these countries have a sufficiently similar mix of initial resource endowments, greater trade openness brings with it a reduction in resources diverted to conflict and thus wasted, as well as the familiar gains from trade. Although a move to trade can otherwise induce greater arming by one country and thus need not be welfare improving for both, aggregate arming falls. By contrast, when the two adversaries do not trade with each other but instead trade with a third (friendly) country, a move from autarky to trade intensifies conflict between the two adversaries, inducing greater arming. With data from the years surrounding the end of the Cold War, we exploit the contrasting implications of trade costs between enemies versus trade costs between friends to provide some suggestive evidence in support of the theory.
Comparison of possibilistic fuzzy local information C-means and possibilistic K-nearest neighbors for synthetic aperture sonar image segmentation

Synthetic aperture sonar (SAS) imagery can generate high resolution images of the seafloor. Thus, segmentation algorithms can be used to partition the images into different seafloor environments. In this paper, we compare two possibilistic segmentation approaches. Possibilistic approaches allow for the ability to detect novel or outlier environments as well as well known classes. The Possibilistic Fuzzy Local Information C-Means (PFLICM) algorithm has been previously applied to segment SAS imagery. Additionally, the Possibilistic K-Nearest Neighbors (PKNN) algorithm has been used in other domains such as landmine detection and hyperspectral imagery. In this paper, we compare the segmentation performance of a semi-supervised approach using PFLICM and a supervised method using Possibilistic K-NN. We include final segmentation results on multiple SAS images and a quantitative assessment of each algorithm.
The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy

The major coat proteins of dsDNA tailed phages (order Caudovirales) and herpesviruses form capsids by a mechanism that includes active packaging of the dsDNA genome into a precursor procapsid, followed by expansion and stabilization of the capsid. These viruses have evolved diverse strategies to fortify their capsids, such as non-covalent binding of auxiliary 'decoration' (Dec) proteins. The Dec protein from the P22-like phage L has a highly unusual binding strategy that distinguishes between nearly identical three-fold and quasi-three-fold sites of the icosahedral capsid. Cryo-electron microscopy and three-dimensional image reconstruction were employed to determine the structure of native phage L particles. NMR was used to determine the structure/dynamics of Dec in solution. The NMR structure and the cryo-EM density envelope were combined to build a model of the capsid-bound Dec trimer. Key regions that modulate the binding interface were verified by site-directed mutagenesis.
Correspondence Principles for Effective Dimensions

We show that the classical Hausdorff and constructive dimensions of any union of $\Pi^0_1$-definable sets of binary sequences are equal. If the union is effective, that is, the set of sequences is $\Sigma^0_2$-definable, then the computable dimension also equals the Hausdorff dimension. This second result is implicit in the work of Staiger (1998). Staiger also proved related results using entropy rates of decidable languages. We show that Staiger’s computable entropy rate provides an equivalent definition of computable dimension. We also prove that a constructive version of Staiger’s entropy rate coincides with constructive dimension.
Measuring peer effects in sales research: a review of challenges and remedies

Peers are important sources of influence in the workplace. In addition to a voluminous literature in management, economics, and education on peer effects, a number of sales researchers have documen...
Dynamin Is Required for Efficient Cytomegalovirus Maturation and Envelopment.

ABSTRACT Cytomegalovirus secondary envelopment occurs in a virus-induced cytoplasmic assembly compartment (vAC) generated via a drastic reorganization of the membranes of the secretory and endocytic systems. Dynamin is a eukaryotic GTPase that is implicated in membrane remodeling and endocytic membrane fission events; however, the role of dynamin in cellular trafficking of viruses beyond virus entry is only partially understood. Mouse embryonic fibroblasts (MEF) engineered to excise all three isoforms of dynamin were infected with mouse cytomegalovirus (MCMV-K181). Immediate-early (IE1; m123) viral protein was detected in these triple dynamin knockout (TKO) cells, as well as in mock-induced parental MEF, at early times postinfection, although levels were reduced in TKO cells, indicating that virus entry was affected but not eliminated. Levels of IE1 protein and another viral early protein (m04) were normalized by 48 h postinfection; however, late protein (m55; gB) expression was reduced in infected TKO cells compared to parental MEF. Ultrastructural analysis revealed intact stages of nuclear virus maturation in both cases with equivalent numbers of nucleocapsids containing packaged viral DNA (C-capsids), indicating successful viral DNA replication, capsid assembly, and genome packaging. Most importantly, severe defects in virus envelopment were visualized in TKO cells but not in parental cells. Dynamin inhibitor (dynasore)-treated MEF showed a phenotype similar to TKO cells upon mouse cytomegalovirus infection, confirming the role of dynamin in late maturation processes. In summary, dynamin-mediated endocytic pathways are critical for the completion of cytoplasmic stages of cytomegalovirus maturation. IMPORTANCE Viruses are known to exploit specific cellular functions at different stages of their life cycle in order to replicate, avoid immune recognition by the host and to establish a successful infection. Cytomegalovirus (CMV)-infected cells are characterized by a prominent cytoplasmic inclusion (virus assembly compartment [vAC]) that is the site of virus maturation and envelopment. While endocytic membranes are known to be the functional components of vAC, knowledge of specific endocytic pathways implicated in CMV maturation and envelopment is lacking. We show here that dynamin, which is an integral part of host endocytic machinery, is largely dispensable for early stages of CMV infection but is required at a late stage of CMV maturation. Studies on dynamin function in CMV infection will help us understand the host-virus interaction pathways amenable to targeting by conventional small molecules, as well as by newer generation nucleotide-based therapeutics (e.g., small interfering RNA, CRISPR/CAS gRNA, etc.).
Palladium-Catalyzed Reactions of Enol Ethers: Access to Enals, Furans, and Dihydrofurans

The palladium-catalyzed oxidation of alkyl enol ethers to enals, which employs low loadings of a palladium catalyst, is described. The mild oxidation conditions tolerate a diverse array of functional groups, while allowing the formation of di-, tri-, and tetrasubtituted olefins. The application of this methodology to intramolecular reactions of alkyl enol ethers containing pendant alcohols provides furan and 2,5-dihydrofuran products.
Backflow Transformations via Neural Networks for Quantum Many-Body Wave Functions

Obtaining an accurate ground state wave function is one of the great challenges in the quantum many-body problem. In this Letter, we propose a new class of wave functions, neural network backflow (NNB). The backflow approach, pioneered originally by Feynman and Cohen [Phys. Rev. 102, 1189 (1956)10.1103/PhysRev.102.1189], adds correlation to a mean-field ground state by transforming the single-particle orbitals in a configuration-dependent way. NNB uses a feed-forward neural network to learn the optimal transformation via variational Monte Carlo calculations. NNB directly dresses a mean-field state, can be systematically improved, and directly alters the sign structure of the wave function. It generalizes the standard backflow [L. F. Tocchio et al., Phys. Rev. B 78, 041101(R) (2008)10.1103/PhysRevB.78.041101], which we show how to explicitly represent as a NNB. We benchmark the NNB on Hubbard models at intermediate doping, finding that it significantly decreases the relative error, restores the symmetry of both observables and single-particle orbitals, and decreases the double-occupancy density. Finally, we illustrate interesting patterns in the weights and bias of the optimized neural network.
Potent human immunodeficiency virus type 1 protease inhibitors that utilize noncoded D-amino acids as P2/P3 ligands.

Noncoded D-amino acids have been designed to replace the quinaldic amide-asparaginyl moiety (P 2 /P 3 ligand) found in several potent human immunodeficiency virus (HIV) protease inhibitors such as LY289612. The substituted nitrogen, optimally an N-methanesulfonyl moiety, served as a CH 2 CONH 2 (asparagine side chain mimic), while the amino acid side chain became the backbone and P 3 ligand of these novel inhibitors. Compounds derived from S-aryl-D-cysteine proved to be potent HIV protease inhibitors which also exhibited potent whole cell antiviral activity. Oxidation of the cysteines to the sulfoxide or sulfone oxidation states resulted in significant improvements in potency. For example, the compound derived from N-(methyl-sulfonyl)-2-S-naphthylcysteine sulfone, 17c, was a 3.5 nM inhibitor of HIV protease which inhibited the spread of virus in MT4 cells with an IC 50 = 4.3 nM. Compounds 17c,g,i were found to be orally bioavailable in a rat model.
Syntheses, structures, physical properties, and electronic properties of some AMUQ3 compounds (A = alkali metal, M = Cu or Ag, Q = S or Se).

The seven new isostructural quaternary uranium chalcogenides KCuUS3, RbCuUS3, RbAgUS3, CsCuUS3, CsAgUS3, RbAgUSe3, and CsAgUSe3 were prepared from solid-state reactions. These isostructural materials crystallize in the layered KZrCuS3 structure type in the orthorhombic space group Cmcm. The structure is composed of UQ6 octahedra and MQ4 tetrahedra that share edges to form 2∞[UMQ3−] layers. These layers stack perpendicular to [010] and are separated by layers of face- and edge-sharing AQ8 bicapped trigonal prisms. There are no Q−Q bonds in the structure, so the formal oxidation states of A/U/M/Q may be assigned as 1+/4+/1+/2−, respectively. CsCuUS3 shows semiconducting behavior with thermal activation energy Ea = 0.14 eV and σ298 = 0.3 S/cm. From single-crystal absorption measurements in the near IR range, the optical band gaps of these compounds are smaller than 0.73 eV. The more diffuse 5f electrons play a much more dominant role in the optical properties of the AMUQ3 compounds than do the 4f electrons i...
Synthesis of a chiral 3,3'-di-tert-butyl-2,2'-bipyrrole

Diethyl 3,3′-di-tert-butyl-4,4′-dimethyl-2,2′-bipyrrole-5,5′-dicarboxylate was synthesized in four steps from ethyl 3,5-dimethyl-1H-pyrrole-2-carboxylate. The CH2 hydrogens of the ethyl ester groups of the former are diastereotopic in the 1H-NMR, consistent with axial chirality of the bipyrrole and restricted rotation about the 2,2′-bipyrrole bond, due to the tert-butyl groups. An X-ray structure of the crystalline target compound shows the pyrrole rings are twisted out of coplanarity by 84.5°.
Binuclear manganese complexes as catalysts in the selective and efficient oxidation of sulfides to sulfones

Abstract The binuclear MnIVMnIV manganese complex 1 catalyzes the periodic acid oxidation of sulfides to sulfones under mild conditions. The reaction was found to be highly selective giving almost quantitative yields of the sulfones even in the presence other easily oxidized groups. Only amines were found to hinder the reaction.
Single Database Private Information Retrieval with Logarithmic Communication.

In this paper, we study the problem of single database private information retrieval, and present schemes with only logarithmic server-side communication complexity. Previously the best result could only achieve polylogarithmic communication, and was based on certain less well-studied assumptions in number theory [CMS99]. On the contrary, our construction is based on Paillier’s cryptosystem [P99], which along with its variants have drawn extensive studies in recent cryptographic researches [PP99, G00, CGGN01, DJ01, CGG02, CNS02, ST02, GMMV03, KT03], and have many important applications (e.g., the Cramer-Shoup CCA2 encryption scheme in the standard model [CS02]). Actually, our schemes can be directly used to implement 1-out-of-N `-bit string oblivious transfer with O(`) sender-side communication complexity (against semi-honest receivers and malicious senders). Note the sender-side communication complexity is independent of N , the constant hidden in the big-O notation is in fact small, and ` is unrestricted. Moreover, We also show a way to do communication balancing between the sender-side and the receiver-side. In addition, we show how to handle malicious receivers with small communication overheads, which itself is a non-trivial result.
An AFM study of the properties of passive films on iron surfaces

The electrochemical corrosion processes of iron in a borate solution have been investigated by in situ electrochemical atomic force microscopy (ECAFM). A freshly polished iron surface is easily passivated electrochemically in a borate solution to give a film which is different from the oxide layer which forms on the iron surface in air. Most areas of the passive film are uniform, but some defects still exist in the film which allow localized corrosion to occur. In situ ECAFM can be used to examine these defects directly and to observe the initial corrosion processes in which ferric oxide particles are both formed and reduced by cyclic voltammetry.
π-Stacking Interactions in cis-Bisfullerene[60] Adducts of 6,13-Disubstituted Pentacenes

Experimental, molecular modeling, and model compound studies suggest that favorable fullerene[60] π-stacking interactions in the ground state and in syn-transition states account for the high cis stereoselectivities observed in the reactions between C60 and 6,13-disubstituted pentacenes.
A high-throughput RNA-seq approach to profile transcriptional responses

In recent years RNA-seq protocols have been developed to investigate a variety of biological problems by measuring the abundance of different RNAs. Many study designs involve performing expensive preliminary studies to screen or optimize experimental conditions. Testing a large number of conditions in parallel may be more cost effective. For example, analyzing tissue/environment-specific gene expression generally implies screening a large number of cellular conditions and samples, without prior knowledge of which conditions are most informative (e.g., some cell types may not respond to certain treatments). To circumvent these challenges, we have established a new two-step high-throughput RNA-seq approach: the first step consists of gene expression screening of a large number of conditions, while the second step focuses on deep sequencing of the most relevant conditions (e.g., largest number of differentially expressed genes). This study design allows for a fast and economical screen in step one, with a more efficient allocation of resources for the deep sequencing of the most biologically relevant libraries in step two. We have applied this approach to study the response to 23 treatments in three lymphoblastoid cell lines demonstrating that it should also be useful for other high-throughput transcriptome profiling applications requiring iterative refinement or screening.
Cyclization of unsaturated amides with triflic anhydride and samarium diiodide

Abstract A new approach to the generation of acyl radical equivalents has been developed. Treatment of amides with triflic anhydride followed by samarium diiodide allows for cyclization onto appropriately substituted olefins.
Dearomatization of furans via [2,3]-Still–Wittig rearrangement

Abstract Furans and benzofurans of type 1 were dearomatized via the [2,3]-Still–Wittig rearrangement. Enol ethers 2 could be isolated or isomerized to the corresponding furans 3 . The substitution pattern at the homofuranylic position had a strong influence on reaction behavior. Benzofurans rearranged with the greatest efficiency, and employment of a 3-substituted benzofuran ( 1 ; R′=CH 3 ) allowed the creation of a quaternary carbon center.
Ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryotomography

Bacterial nanowires have garnered recent interest as a proposed extracellular electron transfer (EET) pathway that links the bacterial electron transport chain to solid-phase electron acceptors away from the cell. Recent studies showed that Shewanella oneidensis MR-1 produces outer membrane (OM) and periplasmic extensions that contain EET components and hinted at their possible role as bacterial nanowires. However, their fine structure and distribution of cytochrome electron carriers under native conditions remained unclear, making it difficult to evaluate the potential electron transport (ET) mechanism along OM extensions. Here, we report high-resolution images of S. oneidensis OM extensions, using electron cryotomography (ECT). We developed a robust method for fluorescence light microscopy imaging of OM extension growth on electron microscopy grids and used correlative light and electron microscopy to identify and image the same structures by ECT. Our results reveal that S. oneidensis OM extensions are dynamic chains of interconnected outer membrane vesicles (OMVs) with variable dimensions, curvature, and extent of tubulation. Junction densities that potentially stabilize OMV chains are seen between neighboring vesicles in cryotomograms. By comparing wild type and a cytochrome gene deletion mutant, our ECT results provide the likely positions and packing of periplasmic and outer membrane proteins consistent with cytochromes. Based on the observed cytochrome packing density, we propose a plausible ET path along the OM extensions involving a combination of direct hopping and cytochrome diffusion. A mean-field calculation, informed by the observed ECT cytochrome density, supports this proposal by revealing ET rates on par with a fully packed cytochrome network.
Chromatin Modifiers Alter Recombination Between Divergent DNA Sequences.

Recombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In baker’s yeast, such antirecombination mechanisms can be initiated by the recognition of DNA mismatches in heteroduplex DNA by MSH proteins, followed by recruitment of the Sgs1-Top3-Rmi1 helicase–topoisomerase complex to unwind the recombination intermediate. We previously showed that the repair/rejection decision during single-strand annealing recombination is temporally regulated by MSH (MutShomolog) protein levels and by factors that excise nonhomologous single-stranded tails. These observations, coupled with recent studies indicating that mismatch repair (MMR) factors interact with components of the histone chaperone machinery, encouraged us to explore roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. This work involved the use of an inverted repeat recombination assay thought to measure sister chromatid repair during DNA replication. Our observations are consistent with the histone chaperones CAF-1 and Rtt106, and the histone deacetylase Sir2, acting to suppress heteroduplex rejection and the Rpd3, Hst3, and Hst4 deacetylases acting to promote heteroduplex rejection. These observations, and double-mutant analysis, have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with MMR factors that mediate heteroduplex rejection.