cssi/SciSciGPT-SciSciNet huggingface dataset:
A New Look at Patent Quality: Relating Patent Prosecution to Validity

The article uses two hand-collected data sets to implement a novel research design for analyzing the precursors to patent quality. Operationalizing patent “quality” as legal validity, the article analyzes the relation between Federal Circuit decisions on patent validity and three sets of data about the patents: quantitative features of the patents themselves, textual analysis of the patent documents, and data collected from the prosecution histories of the patents. The article finds large and statistically significant relations between ex post validity and both textual features of the patents and ex ante aspects of the prosecution history (especially prior art submissions and the existence of internal patent office appeals before issuance). The results demonstrate the importance of refocusing analysis of patent quality on replicable indicators like validity, and the value that more comprehensive collection of prosecution history data can have for improving the output of the patent prosecution process.
Performance Standards and Employee Effort: Evidence from Teacher Absences

The 2001 No Child Left Behind Act (NCLB) increased accountability pressure in U.S. public schools by threatening to impose sanctions on Title-1 schools that failed to make adequate yearly progress (AYP) in consecutive years. Difference-in-difference estimates of the effect of failing AYP in the first year of NCLB on teacher effort in the subsequent year suggest that on average, teacher absences in North Carolina fell by about 10 percent. The probability of being frequently absent similarly decreased. These reductions in teacher absences were driven by within-teacher increases in effort and by teachers in the bottom half of the effectiveness distribution. On average, only a modest amount of the achievement gains attributable to the increased accountability pressure are explained by the corresponding decline in teacher absences.
Pleural effusions in patients with Hodgkin lymphoma: clinical predictors and associations with outcome

Pleural effusions are common in Hodgkin lymphoma (HL). However, little is known about their prognostic significance. One hundred and ten patients with HL who presented to the University of Rochester from 1 January 2003 to 12 December 2010 were reviewed. Pleural effusions were evaluated on review of diagnostic-quality computed tomography (CT) scans. Pleural effusions were present in 26/110 patients: 1/7 (14%) stage I, 11/61 (18%) stage II, 3/18 (17%) stage III and 11/24 (46%) stage IV, and 25/91 (27%) patients had mediastinal involvement, 16/38 (42%) patients had extranodal involvement (any) and 5/14 (35%) patients had E lesions (direct extension to extranodal tissue). Unilateral and bilateral pleural effusions were equally prevalent. Survival analysis demonstrated decreased overall survival for patients with pleural effusions of borderline significance for stage I-IV (p = 0.055) but failed to show significance for patients with stage I-III (p = 0.115). Increasing stage, any extranodal involvement and bulky mediastinal disease were each predictive of pleural effusions. The presence of pleural effusion at presentation may be predictive of inferior survival for patients with Hodgkin lymphoma.
Convex Relaxation for Optimal Power Flow Problem: Mesh Networks

This paper is concerned with the optimal power flow (OPF) problem. We have recently shown that a convex relaxation based on semidefinite programming (SDP) is able to find a global solution of OPF for IEEE benchmark systems, and moreover this technique is guaranteed to work over acyclic (distribution) networks. The present work studies the potential of the SDP relaxation for OPF over mesh (transmission) networks. First, we consider a simple class of cyclic systems, namely weakly-cyclic networks with cycles of size 3. We show that the success of the SDP relaxation depends on how the line capacities are modeled mathematically. More precisely, the SDP relaxation is proven to succeed if the capacity of each line is modeled in terms of bus voltage difference, as opposed to line active power, apparent power or angle difference. This result elucidates the role of the problem formulation. Our second contribution is to relate the rank of the minimum-rank solution of the SDP relaxation to the network topology. The goal is to understand how the computational complexity of OPF is related to the underlying topology of the power network. To this end, an upper bound is derived on the rank of the SDP solution, which is expected to be small in practice. A penalization method is then applied to the SDP relaxation to enforce the rank of its solution to become 1, leading to a near-optimal solution for OPF with a guaranteed optimality degree. The remarkable performance of this technique is demonstrated on IEEE systems with more than 7000 different cost functions.
Measuring Partisan Bias in Single‐Member District Electoral Systems

In recent decades, the literature has coalesced around either symmetry or responsiveness as measures of partisan bias in single-member district systems. I argue neither accurately captures the traditional idea of an “efficient” gerrymander, where one party claims more seats without more votes. I suggest a better measure of efficiency and then use this new measure to reconsider a classic study of partisan gerrymandering. Contrary to the original study findings, I show that the effects of party control on bias are small and decay rapidly, suggesting that redistricting is at best a blunt tool for promoting partisan interests.
Carotid Cavernous Fistulae: Indications for Urgent Treatment

Angiographic and clinical data from 155 patients with carotid cavernous fistulae were retrospectively reviewed to determine angiographic features associated with increased risk of morbidity and mortality. These features included presence of a pseudoaneurysm, large varix of the cavernous sinus, venous drainage to cortical veins, and thrombosis of venous outflow pathways distant from the fistula. Clinical signs and symptoms that characterized a hazardous carotid cavernous fistula included increased intracranial pressure, rapidly progressive proptosis, diminished visual acuity, hemorrhage, and transient ischemic attacks. Cortical venous drainage from the carotid cavernous fistula is secondary to occlusion or absence of the normal venous outflow pathways and is associated with signs and symptoms of increased intracranial pressure and an increased risk of intraparenchymal hemorrhage. Angiographic demonstration of a cavernous sinus varix, with extension of the sinus into the subarachnoid space, is associated with an increased risk of fatal subarachnoid hemorrhage. Identification of these high-risk features provides a basis for making decisions about treatment.
High Dimensional Semiparametric Gaussian Copula Graphical Models.

In this paper, we propose a semiparametric approach, named nonparanormal skeptic, for efficiently and robustly estimating high dimensional undirected graphical models. To achieve modeling flexibility, we consider Gaussian Copula graphical models (or the nonparanormal) as proposed by Liu et al. (2009). To achieve estimation robustness, we exploit nonparametric rank-based correlation coefficient estimators, including Spearman's rho and Kendall's tau. In high dimensional settings, we prove that the nonparanormal skeptic achieves the optimal parametric rate of convergence in both graph and parameter estimation. This celebrating result suggests that the Gaussian copula graphical models can be used as a safe replacement of the popular Gaussian graphical models, even when the data are truly Gaussian. Besides theoretical analysis, we also conduct thorough numerical simulations to compare different estimators for their graph recovery performance under both ideal and noisy settings. The proposed methods are then applied on a large-scale genomic dataset to illustrate their empirical usefulness. The R language software package huge implementing the proposed methods is available on the Comprehensive R Archive Network: this http URL r-project.org/.
Bone Morphogenetic Protein Signaling Is Required for Aortic Valve Calcification

Objective—Calcific aortic valve disease (CAVD) is the most prevalent type of heart valve disease, affecting ≈2% of the US population. CAVD is characterized by the presence of calcific nodules, resulting in aortic valve (AoV) stenosis; however, the underlying mechanisms driving disease remain unknown. Studies of human diseased AoV provide initial evidence that bone morphogenetic protein (BMP) signaling, essential for normal bone formation, is activated during CAVD. Mice deficient in Klotho, an FGF23 transmembrane coreceptor, exhibit premature aging and develop AoV calcific nodules as occurs in human CAVD. The role of BMP signaling in the development of CAVD was examined in porcine aortic valve interstitial cells (VICs) and Klotho−/− mice. Approach and Results—We show that activation of BMP signaling, as indicated by pSmad1/5/8 expression, precedes and later localizes with AoV calcification in Klotho−/− mice. In addition, cellular and extracellular matrix changes resembling features of normal bone formation...
Forecasting and Performance: Conceptualizing Forecasting Management Competence as a Higher-Order Construct

This note empirically validates forecasting management competence (FMC) as a higher-order construct based on four underlying sets of practices: internal integration, forecasting process quality, effective use of advanced systems, and evaluation of forecasting. The results from a partial least squares structural equation model support FMC as a significant driver for three outcomes: forecast accuracy, cost reduction, and delivery performance, thereby establishing predictive validity. The study provides insights to the relative effectiveness of the four sets of forecasting practices constituting FMC. A mediator-moderator analysis shows that forecast accuracy is not a mediator or a moderator between FMC and the other two outcome variables of cost reduction and delivery performance. This indicates that in addition to effective demand forecasting practices, other processes such as sales and operations planning (S&OP) are also important for translating the benefits of effective forecasting to realize favorable business outcomes. A multigroup analysis shows that the impact of the four practice elements on the three performance outcomes also differs based on specific business contexts.
Protecting asplenic individuals from fulminant pneumococcal disease.

Rapid communications Case report: Fulminant pneumococcal sepsis in an unvaccinated asplenic patient in Italy 4 by M Chironna, A Sallustio, A De Robertis, M Quarto, C Germinario Syndromic surveillance to assess the potential public health impact of the Icelandic volcanic ash plume across the United Kingdom, April 2010 6 by AJ Elliot, N Singh, P Loveridge, S Harcourt, S Smith, R Pnaiser, K Kavanagh, C Robertson, CN Ramsay, J McMenamin, A Kibble, V Murray, S Ibbotson, M Catchpole, B McCloskey, GE Smith Upsurge of infections caused by Salmonella Concord among Ethiopian adoptees in Denmark, 2009 10 by R Sjogren Hendriksen, C Kjelso, M Torpdahl, S Ethelberg, K Molbak, FM Aarestrup
The Effect of Local Melting of DNA on DNA Loop Formation

Statistical mechanics of double-stranded DNA (dsDNA) is well described by the wormlike chain model (WLC) which assumes a harmonic bending potential. Such smooth bending potential may no longer be valid for large bending angles to form small loops (< 100 bp). Instead, DNA may rely on rare structural transitions such as local melting (opening) of base pairs to lower the energetic cost. In theory, open base pairs called bubbles can increase the looping probability of short DNA molecules by a few orders of magnitude, but a robust experimental validation of this theoretical prediction is lacking. Here, we investigated the correlation between local melting probability and looping dynamics of dsDNA using single-molecule fluorescence resonance energy transfer (FRET). We designed two groups of short DNA molecules with low and high melting probabilities around their center and measured their looping and unlooping rates in equilibrium. Our data allow rigorous tests of meltable wormlike chain (MWLC) models at short length scales for setting the lower limit for the free energy of bubble formation.
Majorana fermions in condensed-matter physics

It is an honor and a pleasure to have been invited to give a talk in this conference celebrating the memory of the late Professor Abdus Salam. To my regret, I did not know Professor Salam personally, but I am very aware of his work and of his impact on my area of specialization, condensed matter physics, both intellectually through his ideas on spontaneously broken symmetry and more practically through his foundation of the ICTP. Since I assume that most of this audience are not specialized in condensed-matter physics, I thought I would talk about one topic which to some extent bridges this field and the particle-physics interests of Salam, namely Majorana fermions (M.F.s). However, as we shall see, the parallels which are often drawn in the current literature may be a bit too simplistic. I will devote most of this talk to a stripped-down exposition of the current orthodoxy concerning M.F.s. in condensed-matter physics and their possible applications to topological quantum computing (TQC), and then at the end briefly indicate why I believe this orthodoxy may be seriously misleading.
THE OUTCOMES OF SELECTIVE ULTRASOUND SCREENING FOR DEVELOPMENTAL DYSPLASIA OF THE HIP ARE NO BETTER THAN CLINICAL SCREENING ALONE: A COHORT STUDY USING A 40-YEAR-OLD HISTORIC CONTROL GROUP

The aim was to compare the efficacy of selective ultrasound-screening (SUSS) for developmental dysplasia of the hip (DDH) to clinical screening alone, by comparing outcomes in a contemporary group with those from a 40 year old cohort. This was a retrospective cohort study. The department9s DDH and surgical databases were used to identify all cases of DDH, and all cases of surgery for DDH during the study period (2009–13). Patients born outside our region, and teratologic cases were excluded from analysis. The Obstetric database provided the total number of live births over the five-year period. This data was used to calculate the incidence of late-diagnosis (age over 3 months) DDH and the rate of surgery for DDH in our region. These results were compared to those of a similar study from our institution published in 1977, after the introduction of universal clinical screening. Relative risk (RR) was calculated for the two groups, and analysed for statistical significance. The incidence of late-diagnosis DDH over the recent 5-year study period was 0.66/1000 live births, compared to 0.6/1000 in the control group. The RR for late-diagnosis DDH was not significantly different between the two groups (RR 1.14, 95% CI 0.6 to 2.2). The rate of surgery for DDH was 0.86/1000, compared to 0.9/1000 live births in the control group. The RR for surgery for DDH in the current study population compared to the historic control was 0.97, but this difference was not statistically significant (95% C.I. 0.57 to 1.68; p=0.92). Despite advances in screening for DDH over the last 40 years, neither the incidence of late diagnosis DDH, nor rates of surgery for DDH in our region have changed. Whilst previous studies have demonstrated that SUSS does not eliminate late-presenting DDH, this study suggests it confers no advantage over clinical screening alone.
Pay for play: the financial value of NCAA football players

We explore the financial value of National Collegiate Athletic Association (NCAA) football recruits and establish a wage schedule based on the star ratings assigned to high school athletes by an in...
Antimicrobial susceptibility and internalization of Salmonella Typhimurium in vacuum‐tumbled marinated beef products

As the incidence of multidrug resistance (MDR) Salmonella enterica serotype Typhimurium is increasing, data regarding the antimicrobial interventions and pathogen internalization in marinated meat products are important. This study evaluated the antimicrobial intervention and internalization of Salm. Typhimurium in marinated beef sirloin steaks. Beef bottom sirloin flaps (IMPS #185A; USDA Select) inoculated (108 log10 CFU ml−1) with Salm. Typhimurium were sprayed (lactic acid (4%) and buffered vinegar (2%)) prior to vacuum-tumbled marination (0·35% sodium chloride and 0·45% sodium tripolyphosphate) for 30 min. Pathogen presence after antimicrobial spray, vacuum-tumbled marination, and translocation was determined by direct plating on Xylose Lysine Deoxycholate (XLD) agar with tryptic soy agar (TSA) overlay. The data imply varied internalization and antimicrobial susceptibility pattern of Salm. Typhimurium in marinated meat. Lactic acid (4%) spray (P < 0·0001) and buffered vinegar (2%; P < 0·0001) reduced surface populations of Salm. Typhimurium on inoculated beef sirloin flaps prior to vacuum marination. However, lactic acid treated sirloin flaps had greater reductions (~2 log10 CFU cm−2) than buffered vinegar when compared with control prior to vacuum marination. However, the translocation of Salm. Typhimurium following vacuum marination was not influenced (P < 0·333) by the application of a surface organic acid spray prior to marination. Significance and Impact of the Study As detailed in the Federal Register FSIS final rule (9 CFR part 317), vacuum-marinated, vacuum-tumbled meat products are not designated as ‘mechanically tenderized’. As such, the internalization and potential survival of Salmonella spp. in marinated beef products is a major concern. These results highlight the internalization of pathogens in vacuum-tumbled meat products and emphasize the importance of considering these products as nonintact. Similarly, these data confirm the efficacy and utility of interventions prior to vacuum-tumbled marination. Further research is needed to identify additional strategies to mitigate internalization and translocation of pathogens into vacuum-marinated meat products.
Costs of Clock-Environment Misalignment in Individual Cyanobacterial Cells

Abstract Circadian rhythms are endogenously generated daily oscillations in physiology that are found in all kingdoms of life. Experimental studies have shown that the fitness of Synechococcus elongatus , a photosynthetic microorganism, is severely affected in non-24-h environments. However, it has been difficult to study the effects of clock-environment mismatch on cellular physiology because such measurements require a precise determination of both clock state and growth rate in the same cell. Here, we designed a microscopy platform that allows us to expose cyanobacterial cells to pulses of light and dark while quantitatively measuring their growth, division rate, and circadian clock state over many days. Our measurements reveal that decreased fitness can result from a catastrophic growth arrest caused by unexpected darkness in a small subset of cells with incorrect clock times corresponding to the subjective morning. We find that the clock generates rhythms in the instantaneous growth rate of the cell, and that the time of darkness vulnerability coincides with the time of most rapid growth. Thus, the clock mediates a fundamental trade-off between growth and starvation tolerance in cycling environments. By measuring the response of the circadian rhythm to dark pulses of varying lengths, we constrain a mathematical model of a population's fitness under arbitrary light/dark schedules. This model predicts that the circadian clock is only advantageous in highly regular cycling environments with frequencies sufficiently close to the natural frequency of the clock.
SUBCAPITAL FX'S: A CHANGING PARADIGM

To properly care for femoral neck fractures, the surgeon must decide which fractures are to be fixed and which fractures will require a prosthesis. In addition, the type of prosthesis, hemiarthroplasty versus total hip arthroplasty must be selected. Total hip arthroplasty is an option in the active elderly. The literature supports internal fixation in non-displaced fractures. Current literature supports the fact that ORIF of displaced femoral neck fractures results in failure and re-operation of 20% to 30%. By considering arthroplasty when the patient has multiple co-morbidities including renal disease, diabetes, rheumatoid arthritis and severe osteoporosis the re-operation rate can be reduced significantly. The single most important factor in preventing failure with fixation is an anatomic reduction. A femoral neck fracture left in varus is doomed to failure and re-operation. A prosthesis should be used in most displaced femoral neck fractures in patients physiologically older than 65. In active elderly patients total hip replacement should be considered. In elderly patients with multiple co-morbidities who are relatively inactive in a nursing home or lower level community ambulators, a hemi-prosthesis should be considered. The decision-making process is always shared with the patient. When a prosthetic replacement is performed, the low level nursing home or community ambulator who is not expected to live longer than six to seven years is a candidate for a cemented hemi-arthroplasty. Studies report a 25% – 30% re-operation rate in hemi-arthroplasty if the patient survives greater than six to seven years. In the active elderly with little co-morbidity, a total hip replacement should be used. This is not only cost effective but provides the best pain relief of any of the options for treatment of displaced femoral neck fractures. Treatment of femoral neck fractures remains a challenge but the surgeon must select the proper treatment based on fracture displacement, physiologic age of the patient as well as co-morbidities of the patient.
Theory of quantum kagome ice and vison zero modes

We derive an effective ${Z}_{2}$ gauge theory to describe the quantum kagome ice (QKI) state that has been observed by Carrasquilla et al. [Nat. Commun. 6, 7421 (2015)] in Monte Carlo studies of the $S=\frac{1}{2}$ kagome XYZ model in a Zeeman field. The numerical results on QKI are consistent with, but do not confirm or rule out, the hypothesis that it is a ${Z}_{2}$ spin liquid. Our effective theory allows us to explore this hypothesis and make a striking prediction for future numerical studies, namely, that symmetry-protected vison zero modes arise at lattice disclination defects, leading to a Curie defect term in the spin susceptibility, and a characteristic $({N}_{\mathrm{dis}}\ensuremath{-}1)ln2$ contribution to the entropy, where ${N}_{\mathrm{dis}}$ is the number of disclinations. Only the ${Z}_{2}$ Ising symmetry is required to protect the vison zero modes. This is remarkable because a unitary ${Z}_{2}$ symmetry cannot be responsible for symmetry-protected degeneracies of local degrees of freedom. We also discuss other signatures of symmetry fractionalization in the ${Z}_{2}$ spin liquid, and phase transitions out of the ${Z}_{2}$ spin liquid to nearby ordered phases.
Membrane distillation model based on heat exchanger theory and configuration comparison

Abstract Improving the energy efficiency of membrane distillation (MD) is essential for its widespread adoption for renewable energy driven desalination systems. Here, an energy efficiency framework for membrane distillation modules is developed based on heat exchanger theory, and with this an accurate but vastly simplified numerical model for MD efficiency and flux is derived. This heat exchanger analogy shows that membrane distillation systems may be characterized using non-dimensional parameters from counter-flow heat exchanger (HX) theory such as effectiveness ( e ) and number of transfer units (NTU). Along with the commonly used MD thermal efficiency ( η ), “MD effectiveness” e should be used to understand the energy efficiency (measured as gained output ratio, GOR) and water vapor flux of single stage membrane distillation systems. GOR increases linearly with η (due to decreasing conduction losses), but increases more rapidly with an increase in e (better heat recovery). Using the proposed theoretical framework, the performance of different single stage MD configurations is compared for seawater desalination. The gap between the membrane and the condensing surface constitutes the major resistance in both air gap (AGMD) and permeate gap (PGMD) systems (75% of the total in AGMD and 50% in PGMD). Reducing the gap resistance by increasing gap conductance (conductive gap MD (CGMD)), leads to an increase in e through an increase in NTU, and only a small decrease in η , resulting in about two times higher overall GOR. GOR of direct contact MD (DCMD) is limited by the size of the external heat exchanger, and can be as high as that of CGMD only if the heat exchanger area is about 7 times larger than the membrane. While MD membrane design should focus on increasing the membrane’s permeability and reducing its conductance to achieve higher η , module design for seawater desalination should focus on increasing e by reducing the major resistance to heat transfer. A simplified model to predict system GOR and water vapor flux of PGMD, CGMD and DCMD, without employing finite difference discretization, is presented. Computationally, the simplified HX model is several orders of magnitude faster than full numerical models and the results from the simplified model are within 11% of the results from more detailed simulations over a wide range of operating conditions.
Scaling memory-augmented neural networks with sparse reads and writes

Neural networks augmented with external memory have the ability to learn algorithmic solutions to complex tasks. These models appear promising for applications such as language modeling and machine translation. However, they scale poorly in both space and time as the amount of memory grows — limiting their applicability to real-world domains. Here, we present an end-to-end differentiable memory access scheme, which we call Sparse Access Memory (SAM), that retains the representational power of the original approaches whilst training efficiently with very large memories. We show that SAM achieves asymptotic lower bounds in space and time complexity, and find that an implementation runs 1,000 x faster and with 3,000x less physical memory than non-sparse models. SAM learns with comparable data efficiency to existing models on a range of synthetic tasks and one-shot Omniglot character recognition, and can scale to tasks requiring 100,000s of time steps and memories. As well, we show how our approach can be adapted for models that maintain temporal associations between memories, as with the recently introduced Differentiable Neural Computer.
EGFL6 Regulates the Asymmetric Division, Maintenance, and Metastasis of ALDH+ Ovarian Cancer Cells

Little is known about the factors that regulate the asymmetric division of cancer stem-like cells (CSC). Here, we demonstrate that EGFL6, a stem cell regulatory factor expressed in ovarian tumor cells and vasculature, regulates ALDH+ ovarian CSC. EGFL6 signaled at least in part via the oncoprotein SHP2 with concomitant activation of ERK. EGFL6 signaling promoted the migration and asymmetric division of ALDH+ ovarian CSC. As such, EGFL6 increased not only tumor growth but also metastasis. Silencing of EGFL6 or SHP2 limited numbers of ALDH+ cells and reduced tumor growth, supporting a critical role for EGFL6/SHP2 in ALDH+ cell maintenance. Notably, systemic administration of an EGFL6-neutralizing antibody we generated restricted tumor growth and metastasis, specifically blocking ovarian cancer cell recruitment to the ovary. Together, our results offer a preclinical proof of concept for EGFL6 as a novel therapeutic target for the treatment of ovarian cancer. Cancer Res; 76(21); 6396-409. ©2016 AACR.
Hip resurfacing: For the right patient and surgeon

Abstract Hip resurfacing offers several advantages over traditional total hip replacement, such as femoral bone preservation, larger head size, higher activity level, and easier revision options. Now, that hip resurfacing has reached a mature state in its practice, there are substantial data that identifies patients who are most likely to benefit from these advantages. There are, however, risks that are inherent to the metal-on-metal articulation of a hip resurfacing implant. For example, there is a danger of edge loading with the hard-on-hard bearing, leading to excess production of wear debris (metallosis). Furthermore, there is the possibility of an immunologic reaction to the metal wear particles, leading to swelling, osteolysis, and potential tissue destruction. Several studies and national registries have found that male patients with a diagnosis of osteoarthritis, good bone quality, large bone size, and normal anatomy are the cohort who has the highest success rate with hip resurfacing. These patients will also likely achieve a higher activity level, making it worthwhile for them to accept the potential risks of a metal-on-metal implant. Hip resurfacing is also generally accepted to be a more technically difficult procedure than traditional hip replacement due to the need to expose the acetabulum while retaining the native femoral head and neck. Therefore, surgeons need special training to be facile with the procedure and sufficient surgical volume to advance beyond the learning curve. The metal-on-metal bearing is less forgiving than other materials and thus the placement of the implant needs to be more precise. Thus, hip resurfacing will have the greatest chance of success in the right patient and when performed by the right surgeon.
Flow-sensitive composition of thread-modular abstract interpretation

We propose a constraint-based flow-sensitive static analysis for concurrent programs by iteratively composing thread-modular abstract interpreters via the use of a system of lightweight constraints. Our method is compositional in that it first applies sequential abstract interpreters to individual threads and then composes their results. It is flow-sensitive in that the causality ordering of interferences (flow of data from global writes to reads) is modeled by a system of constraints. These interference constraints are lightweight since they only refer to the execution order of program statements as opposed to their numerical properties: they can be decided efficiently using an off-the-shelf Datalog engine. Our new method has the advantage of being more accurate than existing, flow-insensitive, static analyzers while remaining scalable and providing the expected soundness and termination guarantees even for programs with unbounded data. We implemented our method and evaluated it on a large number of benchmarks, demonstrating its effectiveness at increasing the accuracy of thread-modular abstract interpretation.
Using violence, seeking votes: Introducing the Militant Group Electoral Participation (MGEP) dataset

In many cases, including some of the most destructive civil conflicts and some of the newest emerging democracies, militant and ex-militant groups form political parties to participate in elections...
Nonlinearity Testing of Capacitance Bridges Using Programmable Capacitors

We report a test method for characterizing nonlinearity of capacitance bridges by employing two programmable capacitors. Results of several typical bridge nonlinearities are presented. Spectral analysis reveals that the bridge nonlinearities have periodic structures and cannot be reduced through data averaging.
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes

Cancer results from the acquisition of somatic driver mutations. Several computational tools can predict driver genes from population-scale genomic data, but tools for analyzing personal cancer genomes are underdeveloped. Here we developed iCAGES, a novel statistical framework that infers driver variants by integrating contributions from coding, non-coding, and structural variants, identifies driver genes by combining genomic information and prior biological knowledge, then generates prioritized drug treatment. Analysis on The Cancer Genome Atlas (TCGA) data showed that iCAGES predicts whether patients respond to drug treatment (P = 0.006 by Fisher’s exact test) and long-term survival (P = 0.003 from Cox regression). iCAGES is available at http://icages.wglab.org .
Equilibrium mappings in polar-isotropic confined active particles

Despite their fundamentally nonequilibrium nature, the individual and collective behavior of active systems with polar propulsion and isotropic interactions (polar-isotropic active systems) are remarkably well captured by equilibrium mapping techniques. Here we examine two signatures of equilibrium systems --the existence of a local free energy function and the independence of the coarse-grained behavior on the details of the microscopic dynamics-- in polar-isotropic active particles confined by hard walls of arbitrary geometry at the one-particle level. We find that boundaries that possess concave regions make the density profile strongly dynamics-dependent and give it a nonlocal dependence on the geometry of the confining box. This in turn constrains the scope of equilibrium mapping techniques in polar-isotropic active systems.
Sexually Dimorphic Differentiation of a C. elegans Hub Neuron Is Cell Autonomously Controlled by a Conserved Transcription Factor

Functional and anatomical sexual dimorphisms in the brain are either the result of cells that are generated only in one sex or a manifestation of sex-specific differentiation of neurons present in both sexes. The PHC neuron pair of the nematode C. elegans differentiates in a strikingly sex-specific manner. In hermaphrodites the PHC neurons display a canonical pattern of synaptic connectivity similar to that of other sensory neurons, but in males PHC differentiates into a densely connected hub sensory neuron/interneuron, integrating a large number of male-specific synaptic inputs and conveying them to both male-specific and sex-shared circuitry. We show that the differentiation into such a hub neuron involves the sex-specific scaling of several components of the synaptic vesicle machinery, including the vesicular glutamate transporter eat-4/VGLUT, induction of neuropeptide expression, changes in axonal projection morphology, and a switch in neuronal function. We demonstrate that these molecular and anatomical remodeling events are controlled cell autonomously by the phylogenetically conserved Doublesex homolog dmd-3, which is both required and sufficient for sex-specific PHC differentiation. Cellular specificity of dmd-3 action is ensured by its collaboration with non-sex-specific terminal selector-type transcription factors, whereas the sex specificity of dmd-3 action is ensured by the hermaphrodite-specific transcriptional master regulator of hermaphroditic cell identity tra-1, which represses the transcription of dmd-3 in hermaphrodite PHC. Taken together, our studies provide mechanistic insights into how neurons are specified in a sexually dimorphic manner.
Analysis of well hydrographs in a karst aquifer: Estimates of specific yields and continuum transmissivities

Abstract Hydrograph analysis techniques have been well developed for hydrographs obtained from streams and springs, where data are cast in terms of total discharge. The data obtained from well hydrographs provide water level versus time; hence, a method of hydrograph analysis is required for situations in which only water level data are available. It is assumed here that three segments on a recession curve from wells in a karst aquifer represent drainage from three types of storage: conduit (C), fracture (F) and matrix (M). Hydrographs from several wells in a karst aquifer are used to estimate the specific yields (Sy) associated with each portion of the aquifer (C, F, M), as well as continuum transmissivities (T). Data from three short injection tests at one well indicate continuum T at this well bore is approximately 5 m2 day−1, and tests at numerous other wells in the aquifer yield results between 1 and 7 m2 day−1. The T estimated with well hydrographs from two storms indicates a T of 9.8 m2 day−1. Well-developed conduit systems in which water levels in wells show a flashy response typically show Sys of 1 × 10−4, 1 × 10−3, and 3 × 10−3 for C, F, and M, respectively. Less well-developed conduit areas show more nearly equal Sys (8.6 × 10−4, 1.3 × 10−3, 3 × 10−3). Areas with no evidence for the presence of conduits have only one, or in some cases two, slopes on the recession curve. In these cases, water-level responses are slow. Recession curves with a single slope represent drainage from only the lower T matrix. Those with two slopes have an additional, more rapid response segment on the recession curve which represents drainage from the higher T, lower Sy, fractures in the system.
F-polynomial formula from continued fractions

Abstract For cluster algebras from surfaces, there is a known formula for cluster variables and F-polynomials in terms of the perfect matchings of snake graphs. If the cluster algebra has trivial coefficients, there is also a known formula for cluster variables in terms of continued fractions. In this paper, we extend this result to cluster algebras with principal coefficients by producing a formula for the F-polynomials in terms of continued fractions.
Distinguishing Rice Genotypes using Morphological, Agronomical,

Complete data on characteristics of a rice variety is very important to race the authenticity of the variety at the field. Sometimes a name of a variety had changed, due to the informal seed distribution among farmers. This could become problem in the property right of the variety. Distinguishing among rice varieties using only morphological and agronomical traits are sometimes not sufficient. Currently, molecular markers such as SSR (Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphism) markers have become available and are powerfull to distinguish rice genotypes. This research was aimed to distinguish nine rice varieties grown by farmers, using morphological characters (47 traits), agronomical characters (9 traits), SSR markers (12 primer pairs, related with important traits of rice plant), and 384 SNP markers, and to compare the effectiveness of each technique in distinguishing among genotypes. A field experiment was conducted in Ranca Jaya village, Patok Beusi, Subang, West Java during Wet Season (WS) of 2011/2012, using a Randomized Complete Block Design in three replications. A modified CTAB method was used to extract DNA for detection using 12 SSR markers and 384 SNP markers. The results revealed that the use of SSR markers that were linked to certain genes was more accurate than that of the SNP markers, agronomic, and morphological characters, in distinguishing differences among the 9 rice genotypes. The complete data of morphologic, agronomic, and molecular are useful to distinguish the authenticity of a variety in order to protect the intelectual property right attached on the variety.
Area, energy, and time assessment for a distributed TPM for distributed trust in IoT clusters

Abstract IoT clusters arise from natural human societal clusters such as a house, an airport, and a highway. IoT clusters are heterogeneous with a need for device to device as well as device to user trust. The IoT devices are likely to be thin computing clients. Due to low cost, an individual IoT device is not built to be fault tolerant through redundancy. Hence the trust protocols cannot take the liveness of a device for granted. In fact, the differentiation between a failing device and a malicious device is difficult from the trust protocol perspective. We present a minimal distributed trust layer based on distributed consensus like operations. These distributed primitives are cast in the context of the APIs supported by a trusted platform module (TPM). TPM with its 1024 bit RSA is a significant burden on a thin IoT design. We use RNS based slicing of a TPM where in each slice resides within a single IoT device. The overall TPM functionality is distributed among several IoT devices within a cluster. The VLSI area, energy, and time savings of such a distributed TMP implementation is assessed. A sliced/distributed TPM is better suited for an IoT environment based on its resource needs. We demonstrate over 90% time reduction, over 3% area reduction, and over 90% energy reduction per IoT node in order to support TPM protocols.
Marine Bioinorganic Chemistry: The Role of Trace Metals in the Oceanic Cycles of Major Nutrients

The bulk of living biomass is chiefly made up of only a dozen ‘major’ elements whose proportions vary within a relatively narrow range in most organisms. A number of trace elements, particularly first row transition metals are also ‘essential’ for the growth of organisms. We begin this chapter by discussing what we know of the concentrations of trace elements in marine microorganisms and of the relevant mechanisms and kinetics of trace-metal uptake. We then review the biochemical role of trace elements in the marine cycles of carbon, nitrogen, phosphorus, and silicon. Using this information, we examine the evidence, emanating from both laboratory cultures and field measurements, relevant to the mechanisms and the extent of control by trace metals of marine biogeochemical cycles. Before concluding with a wistful glimpse of the future of marine bioinorganic chemistry we discuss briefly some paleoceanographic aspects of this new field: how the chemistry of the planet ‘Earth’ – particularly the concentrations of trace elements in the oceans – has evolved since its origin, chiefly as a result of biological processes and how the evolution of life has, in turn, been affected by the availability of essential trace elements.
Incomplete Contracts and Control

Oliver Hart delivered his Prize Lecture on 8 December 2016 at the Aula Magna, Stockholm University.
Does Accounting Conservatism Discipline Qualitative Disclosure? Evidence From Tone Management in the MD&A*

We investigate whether accounting conservatism, which has been found to be effective in constraining management opportunism in other settings, constrains upward tone management (UTM) in the Management's Discussion and Analysis (MD&A) portion of the 10‐K filing. We hypothesize that conservatism makes it harder for managers to opportunistically downplay bad news and magnify good news when discussing current performance. Consistent with this hypothesis, we find that UTM is negatively associated with several accounting conservatism proxies. Additionally, we hypothesize and find that this association is stronger for firms where managers have higher incentives to manipulate tone. In supplemental analyses, we find evidence to suggest that our results are not due to an endogenous relationship between conservatism and UTM. We also find that conservatism neither encourages downward tone management (DTM) nor constrains managers from conveying real information about future good news. Together, our results suggest that accounting conservatism improves disclosure narratives. La prudence comptable regit‐elle l'information qualitative? Donnees relatives a la gestion du ton adopte dans le rapport de gestion Les auteurs se demandent si la prudence comptable, dont l'efficacite a fait ses preuves dans d'autres contextes pour ce qui est de contenir l'opportunisme de la direction, freine la propension a positiver le ton (upward tone management — UTM) dans le rapport de gestion. Ils posent l'hypothese selon laquelle la prudence fait en sorte qu'il est plus difficile pour les gestionnaires d'edulcorer les nouvelles lorsqu'elles sont mauvaises et de les magnifier lorsqu'elles sont bonnes par opportunisme dans l'analyse de la performance actuelle de l'entreprise. Conformement a cette hypothese, les auteurs constatent l'existence d'un lien negatif entre l'UTM et plusieurs indicateurs de prudence comptable. De plus, ils formulent et confirment l'hypothese selon laquelle ce lien est plus fort dans le cas des entreprises dont les gestionnaires sont davantage encourages a manipuler le ton de leurs interventions. Des analyses complementaires semblent indiquer que ces resultats ne sont pas attribuables a une relation endogene entre la prudence et l'UTM. Les auteurs observent egalement que la prudence n'a pour effet ni d'augmenter la propension a edulcorer le ton (downward tone management — DTM), ni d'empecher les gestionnaires de communiquer de l'information reelle au sujet des bonnes nouvelles a venir. Dans leur ensemble, les resultats de l'etude laissent croire que la prudence comptable ameliore le compte rendu descriptif de l'information.
Changing Model Behavior at Test-time using Reinforcement Learning

Machine learning models are often used at test-time subject to constraints and trade-offs not present at training-time. For example, a computer vision model operating on an embedded device may need to perform real-time inference, or a translation model operating on a cell phone may wish to bound its average compute time in order to be power-efficient. In this work we describe a mixture-of-experts model and show how to change its test-time resource-usage on a per-input basis using reinforcement learning. We test our method on a small MNIST-based example.
On Floer homology and the Berge conjecture on knots admitting lens space surgeries

We complete the first step in a two-part program proposed by Baker, Grigsby, and the author to prove that Berge’s construction of knots in the three-sphere which admit lens space surgeries is complete. The first step, which we prove here, is to show that a knot in a lens space with a threesphere surgery has simple (in the sense of rank) knot Floer homology. The second (conjectured) step involves showing that, for a fixed lens space, the only knots with simple Floer homology belong to a simple finite family. Using results of Baker, we provide evidence for the conjectural part of the program by showing that it holds for a certain family of knots. Coupled with work of Ni, these knots provide the first infinite family of non-trivial knots which are characterized by their knot Floer homology. As another application, we provide a Floer homology proof of a theorem of Berge.
The impact of species-neutral stage structure on macroecological patterns

Despite its radical assumption of ecological equivalence between species, neutral biodiversity theory can often provide good fits to species abundance distributions observed in nature. Major criticisms of neutral theory have focused on interspecific differences, which are in conflict with ecological equivalence. However, neutrality in nature is also broken by differences between conspecific individuals at different life stages, which in many communities may vastly exceed interspecific differences between individuals at similar stages. These within-species asymmetries have not been fully explored in species-neutral models, and it is not known whether demographic stage structure affects macroecological patterns in neutral theory. Here, we present a two-stage neutral model where fecundity and mortality change as an individual transitions from one stage to the other. We explore several qualitatively different scenarios, and compare numerically obtained species abundance distributions to the predictions of unstructured neutral theory. We find that abundance distributions are generally robust to this kind of stage structure, but significant departures from unstructured predictions occur if adults have sufficiently low fecundity and mortality. In addition, we show that the cumulative number of births per species, which is distributed as a power law with a 3/2 exponent, is invariant even when the abundance distribution departs from unstructured model predictions. Our findings potentially explain power law-like abundance distributions in organisms with strong demographic structure, such as eusocial insects and humans, and partially rehabilitate species abundance distributions from past criticisms as to their inability to distinguish between biological mechanisms.