bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative predictions from molecular simulations using explicit or implicit interactions
Authors: van der Spoel David , Zhang Jin , Zhang Haiyang 
Published: June 2021

AbstractEquilibrium simulations of molecular systems allow to extract many physicochemical properties. Given an “accurate enough” model, a “large enough” simulation system and “long enough” simulations, such calculations should yield accurate predictions of properties that can be tested by experimental measurements. Non‐equilibrium simulations can be used as a tool to obtain specific properties like viscosity or conductivity, but they have the drawback that in general only one property per simulation is produced. In addition, a range of methods is available for computing free energy differences. We here review the state of the art of using classical simulation models for generating quantitative predictions. Popular force fields have significant predictive power already but there is room for improvement. Bonded force potentials may need to be replaced by more accurate ones to better reproduce vibrational frequencies. Simplification of non‐bonded force terms, such as cut‐offs for electrostatic or dispersion interactions, should be avoided. Routine usage of force field methods will therefore require some tuning of parameters. Despite the extensive toolbox that is available for producing quantitative results, the computational cost of explicit solvent simulation is significant and therefore, approximate methods like implicit solvent models remain popular and are still being developed. Based on fundamental arguments as well as on examples of solvation free energies, host–guest complexation and non‐covalent association of molecules in solution, we conclude that implicit solvents as well as algorithmic simplifications are most useful when validation using experimental data or rigorous theoretical treatments is possible.This article is categorized under:Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo MethodsTheoretical and Physical Chemistry > Statistical MechanicsSoftware > Simulation Methods
Quantification of pharmaceuticals in the sealant fluids of actively used waterless urinals
Authors: Thapa Utsav , Sharma Priyamvada , Hanigan David 
Published: June 2021

AbstractPrior measurements at bench scale revealed that waterless urinal cartridges containing oily sealant fluids are capable of partitioning pharmaceuticals from urine and therefore reducing their concentration in wastewater. We sought to measure pharmaceutical removal from in‐use waterless urinals. We developed a method to quantify pharmaceuticals in the sealant phase, which resulted in 79 ± 30% and 71 ± 30% recovery of eight pharmaceuticals from two sealant fluids, respectively. The method was applied to sealant samples collected over three weeks from in‐use waterless urinals on a university campus. Six of eight pharmaceuticals were present in the sealant samples from 1.4 µg/L to 241 µg/L. Loads of the six pharmaceuticals detected in the sealants were removed from the receiving wastewater from 0.02 µg/day to 3.4 µg/day across the sampling period. The concentration of the pharmaceuticals were similar over time, indicating rapid saturation and washout of the sealant. We also observed relatively rapid loss of sealant at maintenance intervals consistent with the manufacturer's instructions. These findings indicate that while waterless urinals do remove some pharmaceuticals from the wastewater stream, meaningful changes to wastewater concentrations will only result if the sealant fluid and/or the urinal cartridge are significantly modified.Practitioner points

We developed a quantification method for pharmaceuticals in oily waterless urinal sealants.
Pharmaceuticals were present at relatively low concentrations in the sealant phase of two in‐use waterless urinals.
We identify engineering challenges that must be overcome to meaningfully reduce pharmaceutical loads in wastewater with waterless urinals.
Tracking: B
Authors: Walrand Jean 
Published: June 2021

AbstractIn Chapter Tracking: A, we explained the estimation of a random variable based on observations. We also described the Kalman filter and we gave a number of examples. In this chapter, we derive the Kalman filter and explain some of its properties. We also discuss the extended Kalman filter.Section 10.1 explains how to update an estimate as one makes additional observations. Section 10.2 derives the Kalman filter. The properties of the Kalman filter are explained in Sect. 10.3. Section 10.4 shows how the Kalman filter is extended to nonlinear systems.
Perspective and Complements
Authors: Walrand Jean 
Published: June 2021

AbstractWe have explored a number of topics motivated by concrete applications. It is time to stitch together these ideas into a complete panorama. In addition, we provide some complements.Section 15.1 discusses the general question of inference: what can one deduce from observations? Section 15.2 explains the important notion of sufficient statistic: what is the relevant data in a set of observations? Section 15.3 presents the theory of Markov chains where the number of states is infinite. Section 15.4 explains the Poisson process. Section 15.5 discusses the boosting algorithm for choosing among experts. What drug should you further research; what noisy channel should one use? These are examples of multi-armed bandit problems. In such problems one faces the trade-off between exploiting known possibilities versus exploring potentially more rewarding but less well understood alternatives. Section 15.6 explains a key results for such multi-armed bandit problems. Information Theory studies the limits of communication systems: how fast can one transmit bits reliably over a noisy channel? How many bits should be transmitted to convey some information? Section 15.7 introduces some key concepts and results of Information Theory. When estimating the likelihood of errors or the reliability of some estimates, one usually has to calculate bounds on the probability that a random variable exceeds a given value. Section 15.8 discusses some useful probability bounds. Section 15.9 explains the main ideas of the theory of martingales and shows how it provides a proof of the law of large numbers.
Multiplexing: A
Authors: Walrand Jean 
Published: June 2021

AbstractThis chapter explores the fluctuations of random variables away from their mean value. You flip a fair coin 100 times. How likely is it that you get 60 heads? Conversely, if you get 60 heads, how likely is it that the coin is fair? Such questions are fundamental in extracting information from data.In Sect. 3.1, we start by exploring the rate available to a user when a random number of them share a link, as illustrated in Sect. 3.1. Such calculations are central to network provisioning. The main analytical tool is the Central Limit Theorem explained in Sect. 3.2 where Gaussian random variables are also introduced and confidence intervals are defined. To share a common link, devices may be attached to a switch. For instance, the desktop computers in a building are typically connected to a switch that then sends the data to a common high-speed link. We explore the delays that packets face through the buffer of a switch in Sect. 3.3. The analysis uses a Markov chain model of the buffer. To share a wireless radio channel, devices use a multiple access protocol that regulates the transmissions. We study such schemes in Sect. 3.4. We use probabilistic models of the protocols.
Networks: A
Authors: Walrand Jean 
Published: June 2021

AbstractSocial networks connect people and enable them to exchange information. News and rumors spread through these networks. We explore models of such propagations. The technology behind social networks is the internet where packets travel from queue to queue. We explain some key results about queueing networks.Section 5.1 explores a model of how rumors spread in a social network. Epidemiologists use similar models to study the spread of viruses. Section 5.2 explains the cascade of choices in a social network where one person’s choice is influenced by those of people she knows. Section 5.3 shows how seeding the market with advertising or free products affects adoptions. Section 5.4 studies a model of how media can influence the eventual consensus in a social network. Section 5.5 explores the randomness of the consensus in a group. Sections 5.6 and 5.7 present a different class of network models where customers queue for service. Section 5.6 studies a single queue and Sect. 5.7 analyzes a network of queues. Section 5.8 explains a classical optimization problem in a communication network: how to choose the capacities of different links. Section 5.9 discusses the suitability of queueing networks as models of the internet. Section 5.10 presents a classical result about a class of queueing networks known as product-form networks.
Networks—B
Authors: Walrand Jean 
Published: June 2021

AbstractThis chapter provides the derivations of the results in the previous chapter. It also develops the theory of continuous-time Markov chains.Section 6.1 proves the results on the spreading of rumors. Section 6.2 presents the theory of continuous-time Markov chains that are used to model queueing networks, among many other applications. That section explains the relationships between continuous-time and related discrete-time Markov chains. Sections 6.3 and 6.4 prove the results about product-form networks by using a time-reversal argument.
Digital Link—A
Authors: Walrand Jean 
Published: June 2021

AbstractIn a digital link, a transmitter converts bits into signals and a receiver converts the signals it receives into bits. The receiver faces a decision problem that we study in Sect. 7.1. The main tool is Bayes’ Rule. The key notions are maximum a posteriori and maximum likelihood estimates. Transmission systems use codes to reduce the number of bits they need to transmit. Section 7.2 explains the Huffman codes that minimize the expected number of bits needed to transmit symbols; the idea is to use fewer bits for more likely symbols. Section 7.3 explores a commonly used model of a communication channel: the binary symmetric channel. It explains how to calculate the probability of errors. Section 7.4 studies a more complex modulation scheme employed by most smartphones and computers: QAM. Section 7.5 is devoted to a central problem in decision making: how to infer which situation is in force from observations. Does a test reveal the presence of a disease; how to balance the probability of false positive and that of false negative? The main result of that section is the Neyman–Pearson Theorem that the section illustrates with many examples.
Seeing the entanglement wedge
Authors: Levine Adam , Shahbazi-Moghaddam Arvin , Soni Ronak M 
Published: June 2021

Abstract
We study the problem of revealing the entanglement wedge using simple operations. We ask what operation a semiclassical observer can do to bring the entanglement wedge into causal contact with the boundary, via backreaction.In a generic perturbative class of states, we propose a unitary operation in the causal wedge whose backreaction brings all of the previously causally inaccessible ‘peninsula’ into causal contact with the boundary. This class of cases includes entanglement wedges associated to boundary sub-regions that are unions of disjoint spherical caps, and the protocol works to first order in the size of the peninsula. The unitary is closely related to the so-called Connes Cocycle flow, which is a unitary that is both well-defined in QFT and localised to a sub-region. Our construction requires a generalization of the work by Ceyhan & Faulkner to regions which are unions of disconnected spherical caps. We discuss this generalization in the appendix. We argue that this cocycle should be thought of as naturally generalizing the non-local coupling introduced in the work of Gao, Jafferis & Wall.
Estrogen receptor-α signaling in post-natal mammary development and breast cancers
Authors: Rusidzé Mariam , Adlanmérini Marine , Chantalat Elodie , Raymond-Letron I. , Cayre Surya , Arnal Jean-François , Deugnier Marie-Ange , Lenfant Françoise 
Published: June 2021

Abstract17β-estradiol controls post-natal mammary gland development and exerts its effects through Estrogen Receptor ERα, a member of the nuclear receptor family. ERα is also critical for breast cancer progression and remains a central therapeutic target for hormone-dependent breast cancers. In this review, we summarize the current understanding of the complex ERα signaling pathways that involve either classical nuclear “genomic” or membrane “non-genomic” actions and regulate in concert with other hormones the different stages of mammary development. We describe the cellular and molecular features of the luminal cell lineage expressing ERα and provide an overview of the transgenic mouse models impacting ERα signaling, highlighting the pivotal role of ERα in mammary gland morphogenesis and function and its implication in the tumorigenic processes. Finally, we describe the main features of the ERα-positive luminal breast cancers and their modeling in mice.
Ascon v1.2: Lightweight Authenticated Encryption and Hashing
Authors: Dobraunig Christoph , Eichlseder Maria , Mendel Florian , Schläffer Martin 
Published: June 2021

AbstractAuthenticated encryption satisfies the basic need for authenticity and confidentiality in our information infrastructure. In this paper, we provide the specification ofAscon-128 andAscon-128a. Both authenticated encryption algorithms provide efficient authenticated encryption on resource-constrained devices and on high-end CPUs. Furthermore, they have been selected as the “primary choice” for lightweight authenticated encryption in the final portfolio of the CAESAR competition. In addition, we specify the hash functionAscon-Hash, and the extendable output functionAscon-Xof. Moreover, we complement the specification by providing a detailed overview of existing cryptanalysis and implementation results.
A Novel IFITM5 Variant Associated with Phenotype of Osteoporosis with Calvarial Doughnut Lesions: A Case Report
Authors: Mäkitie R. E. , Pekkinen M. , Morisada N. , Kobayashi D. , Yonezawa Y. , Nishimura G. , Ikegawa S. , Mäkitie O. 
Published: June 2021

AbstractOsteogenesis imperfecta (OI) and other decreased bone density disorders comprise a heterogeneous group of heritable diseases with skeletal fragility. Recently, it was discovered that mutations inSGMS2, encoding sphingomyelin synthetase 2, result in aberrant sphingomyelin metabolism and lead to a novel form of OI termed osteoporosis with calvarial doughnut lesions (OP-CDL) with moderate to severe skeletal fragility and variable cranial hyperostotic lesions. This study describes a Japanese family with the skeletal phenotype of OP-CDL. The affected individuals have moderately severe, childhood-onset skeletal fragility with multiple long-bone fractures, scoliosis and bone deformities. In addition, they exhibit multiple CDLs or calvarial bumps with central radiolucency and peripheral radiopacity. However,SGMS2sequencing was normal. Instead, whole-exome sequencing identified a novelIFITM5missense mutation c.143A>G (p.N48S) (classified as a VUS by ACMG).IFITM5encodes an osteoblast-restricted protein BRIL and a recurrent c.-14C>T mutation in its 5' UTR region results in OI type V, a distinctive subtype of OI associated with hyperplastic callus formation and ossification of the interosseous membranes. The patients described here have a phenotype clearly different from OI type V and with hyperostotic cranial lesions, feature previously unreported in association withIFITM5.Our findings expand the genetic spectrum of OP-CDL, indicate diverse phenotypic consequences of pathogenicIFITM5variants, and imply an important role for BRIL in cranial skeletogenesis.
A novel assay based on pre-equilibrium titration curves for the determination of enzyme inhibitor binding kinetics
Authors: Noppen Bernard , Vanbelle Anouk , Stitt Alan W. , Vanhove Marc 
Published: June 2021

AbstractSelection of pharmacological agents based on potency measurements performed at equilibrium fail to incorporate the kinetic aspects of the drug–target interaction. Here we describe a method for screening or characterization of enzyme inhibitors that allows the concomitant determination of the equilibrium inhibition constant in unison with rates of complex formation and dissociation. The assay is distinct from conventional enzymatic assays and is based on the analysis of inhibition curves recorded prior to full equilibration of the system. The methodology is illustrated using bicyclic peptide inhibitors of the serine protease plasma kallikrein.
A pathological indicator for dysthyroid optic neuropathy: tritan color vision deficiency
Authors: Garip Kuebler Aylin , Halfter Kathrin , Reznicek Lukas , Klingenstein Annemarie , Priglinger Siegfried , Rudolph Günther , Hintschich Christoph 
Published: June 2021

Abstract
Purpose
To investigate the sensitivity of the color vision test by Arden in patients with dysthyroid optic neuropathy (DON) to improve diagnosis.

Methods
In this observational, retrospective study, we included the medical records of 92 eyes (48 patients) with diagnosis of DON between 2008 and 2019 in order to evaluate the full spectrum of findings from the color vision test by Arden, and to determine potential importance of this test. Thirty-five patients were female, and 13 patients were male. The mean age was 58.0 years (range: 34–79) at the time of the DON diagnosis.

Results
Forty-one eyes displayed relatively good BCVA with ≤ 0.2 LogMAR. We found a protan value exceeding the threshold of ≥ 8% in 57 eyes (30 patients) at the time of the diagnosis. The sensitivity of protan was 61.9% (95% CI 51.2–71.8%), while that of tritan was a striking 98.9% (95% CI 94.1–99.9%).
We discovered one pathological sign, tritan deficiency (based on a threshold of ≥ 8%) consistently in all eyes but one at the time of the diagnosis, regardless of the visual field defects or any changes in best-corrected visual acuity (BCVA).

Conclusion
We found blue-yellow (tritan) deficiency, to be a sensitive and reliable indicator of dysthyroid optic neuropathy. We conclude that, in cases with suspected DON, a color vision test that can detect tritan deficiency is an essential tool for the adequate assessment, diagnosis, and treatment of DON.
Pituitary apoplexy induced by gonadotropin-releasing hormone (GnRH) agonist administration for treatment of prostate cancer: a systematic review
Authors: Raj Rishi , Elshimy Ghada , Jacob Aasems , Arya P. V. Akhila , Unnikrishnan Dileep C. , Correa Riccardo , Myint Zin W. 
Published: June 2021

Abstract
Objective
We aimed to review of literature on the clinical presentation, management and outcomes of pituitary apoplexy following gonadotrophic release hormone (GnRH) agonist administration for the treatment of prostate cancer.

Methods
We used PRISMA guidelines for our systematic review and included all English language original articles on pituitary apoplexy following GnRH agonist administration among prostate cancer patients from Jan 1, 1995 to Dec 31, 2020. Data on patient demographics, prostate cancer type, Gleason score at diagnosis, history of pituitary adenoma, clinical presentation, GnRH agonist, interval to pituitary apoplexy, laboratory evaluation at admission, radiologic findings, treatment of pituitary apoplexy, time to surgery if performed, pathology findings, and clinical/hormonal outcomes were collected and analyzed.

Results
Twenty-one patients with pituitary apoplexy met our inclusion criteria. The mean age of patients was 70 (60–83) years. Leuprolide was the most common used GnRH agonist, used in 61.9% of patients. Median duration to symptom onset was 5 h (few minutes to 6 months). Headache was reported by all patients followed by ophthalmoplegia (85.7%) and nausea/vomiting (71.4%). Three patients had blindness at presentation. Only 8 cases reported complete anterior pituitary hormone evaluation on presentation and the most common endocrine abnormality was FSH elevation. Tumor size was described only in 15 cases and the mean tumor size was 26.26 mm (18–48 mm). Suprasellar extension was the most common imaging finding seen in 7 patients. 71.4% of patients underwent pituitary surgery, while 23.8% were managed conservatively. Interval between symptoms onset to pituitary surgery was 7 days (1–90 days). Gonadotroph adenoma was most common histopathologic finding. Clinical resolution was comparable, while endocrine outcomes were variable among patients with conservative vs surgical management.

Conclusion
Although the use of GnRH agonists is relatively safe, it can rarely lead to pituitary apoplexy especially in patients with pre-existing pituitary adenoma. Physicians should be aware of this complication as it can be life threatening. A multidisciplinary team approach is recommended in treating individuals with pituitary apoplexy.
Additional fundophrenicopexia, after Nissen fundoplication, reduces postoperative dysphagia and re-operation rate in the long-term follow up
Authors: Nikolic Milena , Matic Aleksa , Kristo Ivan , Paireder Matthias , Asari Reza , Osmokrovic Bogdan , Semmler Georg , Schoppmann Sebastian F. 
Published: June 2021

AbstractBackgroundVarious technical modifications of Nissen fundoplication (NF) that aim to improve patients’ outcomes have been discussed. This study aims to evaluate the effect of division of the short gastric vessels (SGV) and the addition of a standardized fundophrenicopexia on the postoperative outcome after NF.Methods283 consecutive patients with GERD treated with NF were divided into four groups following consecutive time periods: with division of the SGV and without fundophrenicopexia (group A), with division of the SGV and with fundophrenicopexia (group B), without division of the SGV and with fundophrenicopexia (group C) and without division of the SGV and without fundophrenicopexia (group D). Postoperative contrast swallow, dysphagia scoring, GEDR-HRQL and proton pump inhibitor intake were evaluated. A comparative analysis of patients with division of the SGV and those without (161 A + B vs. 122 C + D), and patients with fundophrenicopexia and those without (78 A vs. 83 B and 49 C vs. 73 D) was performed.ResultsFundophrenicopexia reduced postoperative dysphagia rates (0 group C vs. 5 group D,p = 0.021) in patients where the SGV were preserved and reoperation rates (1 group B vs. 7 group A,p = 0.017) in patients where the SGV were divided. There was no significant difference in the postoperative rates of heartburn relief, dysphagia, gas bloating syndrome, interventions, re-fundoplication and the GERD-HRQL score between groups A + B and C + D, respectively.ConclusionStandardized additional fundophrenicopexia in patients undergoing Nissen fundoplication significantly reduces postoperative dysphagia in patients without division of the SGV and reoperation rates in patients with division of the SGV. Division of the SGV has no influence on the postoperative outcome of NF.