Miracle-dz/UniFAR-FTUs huggingface dataset:
Online Learning with Graph-Structured Feedback against Adaptive Adversaries

We derive upper and lower bounds for the policy regret of $T$-round online learning problems with graph-structured feedback, where the adversary is nonoblivious but assumed to have a bounded memory. We obtain upper bounds of $\mathcal{O}(T^{2/3})$ and $\tilde{\mathrm{O}}(T^{3/4})$ for strongly-observable and weakly-observable graphs, respectively, based on analyzing a variant of the Exp3 algorithm. When the adversary is allowed a bounded memory of size 1, we show that a matching lower bound of $\tilde{\Omega}(T^{2/3})$ is achieved in the case of full-information feedback. We also study the particular loss structure of an oblivious adversary with switching costs, and show that in such a setting, nonrevealing strongly-observable feedback graphs achieve a lower bound of $\tilde{\Omega}(T^{2/3})$, as well.
Dosimetric characteristics of a new linear accelerator under gated operation

Respiratory gated radiotherapy may allow reduction of the treatment margins, thus sparing healthy tissue and/or allowing dose escalation to the tumor. However, current commissioning and quality assurance of linear accelerators do not include evaluation of gated delivery. The purpose of this study is to test gated photon delivery of a Siemens ONCOR Avant‐Garde linear accelerator. Dosimetric characteristics for gated and nongated delivery of 6‐MV and 15‐MV photons were compared for the range of doses, dose rates, and for several gating regimes. Dose profiles were also compared using Kodak EDR2 and X‐Omat V films for 6‐MV and 15‐MV photons for several dose rates and gating regimes. Results showed that deviation is less than or equal to 0.6% for all dose levels evaluated with the exception of the lowest dose delivered at 25 MU at an unrealistically high gating frequency of 0.5 Hz. At 400 MU, dose profile deviations along the central axes in in‐plane and cross‐plane directions within 80% of the field size are below 0.7%. No unequivocally detectable dose profile deviation was observed for 50 MU. Based on the comparison with widely accepted standards for conventional delivery, our results indicate that this LINAC is well suited for gated delivery of nondynamic fields. PACS numbers: 87.56‐By, 87.66‐Cd, 87.66‐Jj
An Eya1-Notch axis specifies bipotential epibranchial differentiation in mammalian craniofacial morphogenesis

Craniofacial morphogenesis requires proper development of pharyngeal arches and epibranchial placodes. We show that the epibranchial placodes, in addition to giving rise to cranial sensory neurons, generate a novel lineage-related non-neuronal cell population for mouse pharyngeal arch development. Eya1 is essential for the development of epibranchial placodes and proximal pharyngeal arches. We identify an Eya1-Notch regulatory axis that specifies both the neuronal and non-neuronal commitment of the epibranchial placode, where Notch acts downstream of Eya1 and promotes the non-neuronal cell fate. Notch is regulated by the threonine phosphatase activity of Eya1. Eya1 dephosphorylates p-threonine-2122 of the Notch1 intracellular domain (Notch1 ICD), which increases the stability of Notch1 ICD and maintains Notch signaling activity in the non-neuronal epibranchial placodal cells. Our data unveil a more complex differentiation program in epibranchial placodes and an important role for the Eya1-Notch axis in craniofacial morphogenesis.
Subcellular analysis of pigeon hair cells implicates vesicular trafficking in cuticulosome formation and maintenance

Hair cells are specialized sensors located in the inner ear that enable the transduction of sound, motion, and gravity into neuronal impulses. In birds some hair cells contain an iron-rich organelle, the cuticulosome, that has been implicated in the magnetic sense. Here, we exploit histological, transcriptomic, and tomographic methods to investigate the development of cuticulosomes, as well as the molecular and subcellular architecture of cuticulosome positive hair cells. We show that this organelle forms rapidly after hatching in a process that involves vesicle fusion and nucleation of ferritin nanoparticles. We further report that transcripts involved in endocytosis, extracellular exosomes, and metal ion binding are differentially expressed in cuticulosome positive hair cells. These data suggest that the cuticulosome and the associated molecular machinery regulate the concentration of iron within the labyrinth of the inner ear, which might indirectly tune a magnetic sensor that relies on electromagnetic induction.
Two-variable Block Dual Coordinate Descent Methods for Large-scale Linear Support Vector Machines

Coordinate descent (CD) methods have been a state-of-the-art technique for training largescale linear SVM. The most used setting is to solve the dual problem of an SVM formulation without the bias term, for which the CD procedure of updating one variable at a time is very simple and easy to implement. In this work, we extend the one-variable setting to use two variables at each CD step. The extension, while looks simple, is not trivial. Some complicated derivations are needed to get a simple CD procedure. Our resulting algorithm is generally competitive with one-variable CD and is superior for difficult problems. We further discuss the two-variable CD for the standard SVM formulation with a bias term. The analysis shows that CD methods are less effective for this SVM formulation, a situation very different from that of kernel SVM. Thus the success of simple one-variable CD in the past decade is not a coincidence. Some design choices such as the SVM formulation considered help to make it computationally efficient. Overall this work sheds many new insights on CD methods for training linear SVM.
Molecular identification of zoonotic hookworm species in dog faeces from Tanzania

Abstract The presence and distribution of various species of canine hookworms in Africa are poorly known. The main objective of this study, therefore, was to identify the hookworm species present in canine faecal samples from Morogoro, Tanzania, using molecular techniques. Faecal samples from 160 local dogs were collected and hookworm positive samples processed to recover larvae for further molecular characterization. DNA was extracted from pools of larvae from individual samples (n = 66), which were analysed subsequently using two different molecular approaches, polymerase chain reaction-linked restriction fragment length polymorphism (PCR-RFLP) and species-specific PCR coupled with Sanger sequencing. The PCR-RFLP technique detected only the presence of the ubiquitous Ancylostoma caninum in the 66 samples. However, by species-specific PCR coupled with Sanger sequencing we identified ten samples with A. braziliense, two with Uncinaria stenocephala and five with A. ceylanicum. Thus, all four known species of canine hookworms were identified in Morogoro, Tanzania. To our knowledge this is the first report of the detection of the presence of U. stenocephala and A. ceylanicum in Africa using molecular techniques. In addition to their veterinary importance, canine hookworms have zoonotic potential and are of public health concern.
Tidal volume measurements in infants: Opto‐electronic plethysmography versus pneumotachograph

Tidal breathing measurements by Opto‐Electronic Plethysmography (OEP) has been reported for infants limited to protocols with two chest wall compartments. Standard protocol for the analysis of adults, with three compartments of chest wall, has been unavailable for analysis of infants. We aimed to study the agreement of simultaneous measurements of tidal volume by OEP (VT,OEP) and a heated pneumotachograph (PNT) (VT,PNT) performed during sleeping in 20 infants (gestational age 35.1 ± 4.6 weeks) at 3–4 months postconceptual age with a three compartment protocol. From PNT and OEP measurements, tidal volume corrected (VT,PNT) for ambient conditions were calculated with a total number of 200 breaths. The two methods were in good agreement with tidal volume mean difference of 0.02 ml and limit of agreement −4.11 to 4.08 ml (95%CI), no relationship was found between differences and means of OEP and PNT measurements. Pulmonary rib cage, abdominal rib cage and abdomen contributed by 12.4 ± 9.7%, 5.2 ± 5.1%, and 82.4 ± 11.4% to VT,OEP, respectively. The OEP experimental protocol based on 52 markers and a three‐compartment model of the chest wall could be used in spontaneously sleeping infants. Pediatr Pulmonol. 2016;51:850–857. © 2016 Wiley Periodicals, Inc.
Early initiation of post-sternotomy cardiac rehabilitation exercise training (SCAR): study protocol for a randomised controlled trial and economic evaluation

Introduction Current guidelines recommend abstinence from supervised cardiac rehabilitation (CR) exercise training for 6 weeks post-sternotomy. This practice is not based on empirical evidence, thus imposing potentially unnecessary activity restrictions. Delayed participation in CR exercise training promotes muscle atrophy, reduces cardiovascular fitness and prolongs recovery. Limited data suggest no detrimental effect of beginning CR exercise training as early as 2 weeks post-surgery, but randomised controlled trials are yet to confirm this. The purpose of this trial is to compare CR exercise training commenced early (2 weeks post-surgery) with current usual care (6 weeks post-surgery) with a view to informing future CR guidelines for patients recovering from sternotomy. Methods and analysis In this assessor-blind randomised controlled trial, 140 cardiac surgery patients, recovering from sternotomy, will be assigned to 8 weeks of twice-weekly supervised CR exercise training commencing at either 2 weeks (early CR) or 6 weeks (usual care CR) post-surgery. Usual care exercise training will adhere to current UK recommendations. Participants in the early CR group will undertake a highly individualised 2–3 week programme of functional mobility, strength and cardiovascular exercise before progressing to a usual care CR programme. Outcomes will be assessed at baseline (inpatient), pre-CR (2 or 6 weeks post-surgery), post-CR (10 or 14 weeks post-surgery) and 12 months. The primary outcome will be change in 6 min walk distance. Secondary outcomes will include measures of functional fitness, quality of life and cost-effectiveness. Ethics and dissemination Recruitment commenced on July 2017 and will complete by December 2019. Results will be disseminated via national governing bodies, scientific meetings and peer-reviewed journals. Trial registration number NCT03223558; Pre-results.
Interplay of PA-X and NS1 Proteins in Replication and Pathogenesis of a Temperature-Sensitive 2009 Pandemic H1N1 Influenza A Virus

ABSTRACT Influenza A viruses (IAVs) cause seasonal epidemics and occasional pandemics, representing a serious public health concern. It has been described that one mechanism used by some IAV strains to escape the host innate immune responses and modulate virus pathogenicity involves the ability of the PA-X and NS1 proteins to inhibit the host protein synthesis in infected cells. It was reported that for the 2009 pandemic H1N1 IAV (pH1N1) only the PA-X protein had this inhibiting capability, while the NS1 protein did not. In this work, we have evaluated, for the first time, the combined effect of PA-X- and NS1-mediated inhibition of general gene expression on virus pathogenesis, using a temperature-sensitive, live-attenuated 2009 pandemic H1N1 IAV (pH1N1 LAIV). We found that viruses containing PA-X and NS1 proteins that simultaneously have (PAWT+/NS1MUT+) or do not have (PAMUT−/NS1WT−) the ability to block host gene expression showed reduced pathogenicity in vivo. However, a virus where the ability to inhibit host protein expression was switched between PA-X and NS1 (PAMUT−/NS1MUT+) presented pathogenicity similar to that of a virus containing both wild-type proteins (PAWT+/NS1WT−). Our findings suggest that inhibition of host protein expression is subject to a strict balance, which can determine the successful progression of IAV infection. Importantly, knowledge obtained from our studies could be used for the development of new and more effective vaccine approaches against IAV. IMPORTANCE Influenza A viruses (IAVs) are one of the most common causes of respiratory infections in humans, resulting in thousands of deaths annually. Furthermore, IAVs can cause unpredictable pandemics of great consequence when viruses not previously circulating in humans are introduced into humans. The defense machinery provided by the host innate immune system limits IAV replication; however, to counteract host antiviral activities, IAVs have developed different inhibition mechanisms, including prevention of host gene expression mediated by the viral PA-X and NS1 proteins. Here, we provide evidence demonstrating that optimal control of host protein synthesis by IAV PA-X and/or NS1 proteins is required for efficient IAV replication in the host. Moreover, we demonstrate the feasibility of genetically controlling the ability of IAV PA-X and NS1 proteins to inhibit host immune responses, providing an approach to develop more effective vaccines to combat disease caused by this important respiratory pathogen.
Fast Evaluation of Homomorphic Encryption Schemes Based on Ring-LWE

When evaluating Homomorphic Encryption (HE) schemes, only one set of input parameters is usually considered. Evaluation reports HE scheme time execution and memory consumption since these are the main challenges of HE. The original version of PAnTHErS enables to evaluate HE schemes without executing the scheme, hence with a very low processing time (< 10 sec). Results are provided in terms of computational complexity and memory cost. This allows to evaluate a scheme for numerous sets of input parameters. In this paper, PAnTHErS is improved by a calibration phase, and four HE schemes based on Ring-LWE are analyzed and compared using the proposed tool. Experimentation results show the approach allows analyses of HE scheme with an average of 6% error for a given implementation with a speedup up to 15× compared to actual scheme executions.
SNP genetic polymorphisms of MDR-1, CYP1A2 and CYPB11 genes in four canine breeds upon toxicological evaluation

The fields of pharmacogenetics and pharmacogenomics have become increasingly promising regarding the clinical application of genetic data to aid in prevention of adverse reactions. Specific screening tests can predict which animals express modified proteins or genetic sequences responsible for adverse effects associated with a drug. Among the genetic variations that have been investigated in dogs, the multidrug resistance gene (MDR) is the best studied. However, other genes such as CYP1A2 and CYP2B11 control the protein syntheses involved in the metabolism of many drugs. In the present study, the MDR-1, CYP1A2 and CYP2B11 genes were examined to identify SNP polymorphisms associated with these genes in the following four canine breeds: Uruguayan Cimarron, Border Collie, Labrador Retriever and German Shepherd. The results revealed that several SNPs of the CYP1A2 and CYP2B11 genes are potential targets for drug sensitivity investigations.
Overview and Latest Developments in Photoconductance Lifetime Measurements in Silicon

Photoconductance measurements have been one of the most common ways to measure the lifetime in silicon for over 60 years. Since 1985, the most common method for doing calibrated lifetime measurements is using an eddy-current sensor to monitor photoconductance as a function of time and illumination, providing data that can be interpreted in terms of carrier density and hence lifetime. Here we present recent extensions to this measurement technique that have generalized the method. Bulk lifetime measurements on industrial samples are presented. The information available from the effects of grain boundaries on eddy-current measurements are summarized. Recent applications for the use of these instruments for measurement of mobility in compensated materials are also described.
Combining Mental Training and Physical Training With Goal-Oriented Protocols in Stroke Rehabilitation: A Feasibility Case Study

Stroke is one of the leading causes of permanent disability in adults. The literature suggests that rehabilitation is key to early motor recovery. However, conventional therapy is labor and cost intensive. Robotic and functional electrical stimulation (FES) devices can provide a high dose of repetitions and as such may provide an alternative, or an adjunct, to conventional rehabilitation therapy. Brain-computer interfaces (BCI) could augment neuroplasticity by introducing mental training. However, mental training alone is not enough; but combining mental with physical training could boost outcomes. In the current case study, a portable rehabilitative platform and goal-oriented supporting training protocols were introduced and tested with a chronic stroke participant. A novel training method was introduced with the proposed rehabilitative platform. A 37-year old individual with chronic stroke participated in 6-weeks of training (18 sessions in total, 3 sessions a week, and 1 h per session). In this case study, we show that an individual with chronic stroke can tolerate a 6-week training bout with our system and protocol. The participant was actively engaged throughout the training. Changes in the Wolf Motor Function Test (WMFT) suggest that the training positively affected arm motor function (12% improvement in WMFT score).
Towards automated planning for unsealed source therapy

The purpose of this study was to develop and validate a technique for unsealed source radiotherapy planning that combines the segmentation and registration tasks of single‐photon emission tomography (SPECT) and computed tomography (CT) datasets. The segmentation task is automated by an atlas registration approach that takes advantage of a hybrid scheme using a diffeomorphic demons algorithm to warp a standard template to the patient's CT. To overcome the lack of common anatomical features between the CT and SPECT datasets, registration is achieved through a narrow band approach that matches liver contours in the CT with the gradients of the SPECT dataset. Deposited dose is then computed from the SPECT dataset using a convolution operation with tracer‐specific deposition kernels. Automatic segmentation showed good agreement with manual contouring, measured using the dice similarity coefficient and ranging from 0.72 to 0.87 for the liver, 0.47 to 0.93 for the kidneys, and 0.74 to 0.83 for the spinal cord. The narrow band registration achieved variations of less 0.5 mm translation and 1° rotation, as measured with convergence analysis. With the proposed combined segmentation–registration technique, the uncertainty of soft‐tissue target localization is greatly reduced, ensuring accurate therapy planning. PACS number: 87.55. de, 87.55. kd
ELECTRON BEAM LOSS IN COMMERCIAL ESEM

Conventional differential pumping is used on present day commercial environmental scanning electron microscope (ESEM) instruments to separate the high vacuum of the electron optics column from the high pressure specimen chamber. A transition region of intermediate pressures is established between the two extreme regions of the microscope. The electron beam is transferred from the high vacuum to the high pressure via a transition region in which the beam undergoes collisions with the gas and suffers initial electron losses. The loss of electrons in the transition region is an inevitable consequence of the differential pumping method used. In particular, the magnitude of electron loss is determined by the design of a given instrument and can be greater or equal to some physical limit imposed by the formation of a supersonic gas jet downstream of the pressure-limiting aperture (PLA).
Faint Blue Objects in the Hubble Deep Field-South Revealed: White Dwarfs, Subdwarfs, and Quasars

We explore the nature of the faint blue objects in the Hubble Deep Field-South. We have derived proper motions for the point sources in the Hubble Deep Field-South using a 3 yr baseline. Combining our proper-motion measurements with spectral energy distribution fitting enabled us to identify four quasars and 42 stars, including three white dwarf candidates. Two of these white dwarf candidates, HDF-S 1444 and 895, are found to display significant proper motion, 21.1 ± 7.9 and 34.9 ± 8.0 mas yr-1, and are consistent with being thick-disk or halo white dwarfs located at ~2 kpc. The other faint blue objects analyzed by Mendez & Minniti do not show any significant proper motion and are inconsistent with being halo white dwarfs; they do not contribute to the Galactic dark matter. The observed population of stars and white dwarfs is consistent with standard Galactic models.
Efficient protein targeting to the inner nuclear membrane requires Atlastin-dependent maintenance of ER topology

Newly synthesized membrane proteins are targeted to the inner nuclear membrane (INM) by diffusion within the membrane system of the endoplasmic reticulum (ER), translocation through nuclear pore complexes (NPCs) and retention on nuclear partners. Using a visual in vitro assay we previously showed that efficient protein targeting to the INM depends on nucleotide hydrolysis. We now reveal that INM targeting is GTP-dependent. Exploiting in vitro reconstitution and in vivo analysis of INM targeting, we establish that Atlastins, membrane-bound GTPases of the ER, sustain the efficient targeting of proteins to the INM by their continued activity in preserving ER topology. When ER topology is altered, the long-range diffusional exchange of proteins in the ER network and targeting efficiency to the INM are diminished. Highlighting the general importance of proper ER topology, we show that Atlastins also influence NPC biogenesis and timely exit of secretory cargo from the ER.
Development of a Platform-Independent Software Tool for Management of X.509 Certificates from Diverse Certificate Stores

The ongoing digitization in the healthcare sector initiates collecting and processing medical data in electronic form. However, for a long time there has been a search for a safe and legally compliant solution that contributes to the exchange of patient data. The goal of this project is to develop a platform-independent software for the management of X.509-certificates across different certificate stores. The current work addresses the gap in transparent digital certificate management of the various operating systems and applications. To the best of our knowledge, it is the first to offer such features and functionality. The developed system provides a trustworthy solution for more secure management of sensitive healthcare data and improves the overall satisfaction in the modern structures and work processes utilized in healthcare.