Miracle-dz/UniFAR-FTUs huggingface dataset:
A new test and graphical tool to assess the goodness of fit of logistic regression models

A prognostic model is well calibrated when it accurately predicts event rates. This is first determined by testing for goodness of fit with the development dataset. All existing tests and graphic tools designed for the purpose suffer several drawbacks, related mainly to the subgrouping of observations or to heavy dependence on arbitrary parameters. We propose a statistical test and a graphical method to assess the goodness of fit of logistic regression models, obtained through an extension of similar techniques developed for external validation. We analytically computed and numerically verified the distribution of the underlying statistic. Simulations on a set of realistic scenarios show that this test and the well‐known Hosmer–Lemeshow approach have similar type I error rates. The main advantage of this new approach is that the relationship between model predictions and outcome rates across the range of probabilities can be represented in the calibration belt plot, together with its statistical confidence. By readily spotting any deviations from the perfect fit, this new graphical tool is designed to identify, during the process of model development, poorly modeled variables that call for further investigation. This is illustrated through an example based on real data. Copyright © 2015 John Wiley & Sons, Ltd.
Key factors regulating Plasmodium berghei sporozoite survival and transformation revealed by an automated visual assay

Malaria is transmitted to the host when Plasmodium sporozoites are injected by a mosquito vector. Sporozoites eventually enter hepatocytes, where they differentiate into liver‐stage parasites. During the first hours after hepatocyte invasion, the crescent‐shaped sporozoites transform into spherical intracellular exoerythrocytic parasites. This process, which precedes genome replication, can be mimicked in vitro in the absence of host cells. Here, we developed an automated method to follow transformation and cell death of sporozoites in vitro. This assay provides a rapid tool to test sporozoite survival and to screen for antiparasitic drugs. We found that extracellular bicarbonate and high temperature trigger transformation, whereas physiological serum albumin concentrations and media lacking bicarbonate delayed sporozoite death. Because bicarbonate also triggers ookinete transformation and exflagellation of gametocytes, we suggest that a common molecular mechanism regulates similar aspects of stage conversion in Plasmodium. —Hegge, S. , Kudryashev, M. , Barniol, L. , Frischknecht, F. Key factors regulating Plasmodium berghei sporozoite survival and transformation revealed by an automated visual assay. FASEB J. 24, 5003–5012 (2010). www.fasebj. org
Edema of the spinal cord following experimental impact trauma.

✓ Identification of central nervous system edema is based on increased water content in relation to nonvolatile residue per unit weight. Nonvolatile residue in spinal cord tissue following impact trauma was determined to ascertain the magnitude and persistence of edema. High and low thoracic laminectomies were carried out on each of 17 rhesus monkeys. The lower exposed cord was traumatized with a calibrated blow of 300 gm cm. All upper exposed cords and the lower exposed cord in one monkey served as nontraumatized controls. At time intervals of 5 minutes to 20 days after trauma, cord segments were removed and assayed for water content. Increased tissue water was evident within 5 minutes and persisted for 15 days. By the 20th day it had essentially subsided. Increased tissue water content in the traumatized segment reached a maximum of 7.4% over control values at 5 days and then gradually diminished. These findings support the concept that edema following spinal trauma is unrelated to secondary effects of .
Intrabronchial Microdialysis: Effects of Probe Localization on Tissue Trauma and Drug Penetration into the Pulmonary Epithelial Lining Fluid

Recent intrabronchial microdialysis data indicate that the respiratory epithelium is highly permeable to drugs. Of concern is whether intrabronchial microdialysis disrupts the integrity of the respiratory epithelium and thereby alters drug penetration into the pulmonary epithelial lining fluid (PELF). The objective of this study was to investigate the effect of intrabronchial microdialysis on the integrity of the bronchial epithelium. Microdialysis sampling in PELF in proximal (n = 4) and distal bronchi (n = 4) was performed after intravenous inulin and florfenicol administration in anaesthetized pigs. Inulin was used as a marker molecule of permeability of the epithelium, and florfenicol was used as test drug. Bronchial tissue was examined by histopathology (distal and proximal bronchi) and gene expression analysis (RT‐qPCR, proximal bronchi) at the termination of the experiment (6.5 hr). The microdialysis probe caused overt tissue trauma in distal bronchi, whereas no histopathological lesions were observed in proximal bronchi. A moderate up‐regulation of the pro‐inflammatory cytokines IL1B, IL6 and acute‐phase reactant serum amyloid A was seen in proximal bronchi surrounding the microdialysis probes suggesting initiation of an inflammatory response. The observed up‐regulation is considered to have limited impact on drug penetration during short‐term studies. Inulin penetrated the respiratory epithelium in both proximal and distal bronchi without any correlation to histopathological lesions. Likewise, florfenicol penetration into PELF was unaffected by bronchial histopathology. However, this independency of pathology on drug penetration may not be valid for other antibiotics. We conclude that short‐term microdialysis drug quantification can be performed in proximal bronchi without disruption of tissue integrity.
PCR-RFLP Based Method for Molecular Differentiation of Sand Fly Species Phlebotomus argentipes, Phlebotomus papatasi, and Sergentomyia babu Found in India

ABSTRACT PCR-Restriction fragment length polymorphism is a time saving and accurate technique to differentiate closely related organisms. In the regions endemic for visceral leishmaniasis in India, various species of morphological similar sand fly exist but only female Phlebotomus argentipes is the vector for visceral leishmaniasis. In the current study primers were designed targeting the 18S rRNA encoding gene that showed amplification in all the major sand fly species found in India. The amplified fragments were further digested using the HinfI or HpaII restriction enzymes. Each of the restriction enzyme produced a species specific restriction patterns, which can easily be used to identify specific sand fly species. This technique can be used in the identification of sand fly species.
Poster abstract: neighborhood-based power management

Given the constrained energy resources of sensor nodes, many power management protocols have been proposed to manage sleep and duty cycles to reduce energy during idle times in communication. Such scheduling in a sensor network can be determined by either the receiver or the sender. In a receiver-driven protocol, the receiver indicates its wakeup schedule to potential senders in its neighborhood. In a senderdriven protocol, the sender indicates to its receiver that it should remain awake to receive upcoming data. Receiver-driven protocols, such as IEEE 802.11 PSM [1], S-MAC [3] and SCP-MAC [4], allow nodes to synchronize their sleep schedules. Since a sender knows when a receiver will be awake to receive data, these protocols reduce the time nodes spend in idle listening. However, nodes must exchange schedule information with their neighbors to enable such synchronization. This synchronization cost can be amortized if there is high data traffic. However, when data traffic is low, synchronization costs dominate energy consumption in the network, reducing network lifetime. Sender-driven protocols such as B-MAC [2] avoid this cost by not requiring the neighbor nodes to synchronize. However, the sender must signal the receiver for every packet, adding significant overhead in networks with higher data rates. The goal of our research is to take the lessons learned from both receiver-driven and sender-driven protocols and design a new power management protocol that can save energy in networks with both high and low data rates. Our approach is based on the observation that the signalling in sender-driven protocols not only wakes up the receiver, but also wakes up all nodes in transmission range of the sender. The nonreceiver nodes waste energy listening to the sender’s signal. Additionally, they go back to sleep after the signal, even if they have some data of their own to send. Our protocol, called Neighborhood-based Power Management (NPM), innovatively combines sender-driven and receiver-driven techniques to leverage the advantages of both ends. Our evaluation reflects the advantage. By allowing neighbors of the signalling node to send data opportunistically, our protocol not only conserves energy, but also improves delay.
Differentiation rather than aging of muscle stem cells abolishes their telomerase activity

A general feature of stem cells is the ability to routinely proliferate to build, maintain, and repair organ systems. Accordingly, embryonic and germline, as well as some adult stem cells, produce the telomerase enzyme at various levels of expression. Our results show that, while muscle is a largely postmitotic tissue, the muscle stem cells (satellite cells) that maintain this biological system throughout adult life do indeed display robust telomerase activity. Conversely, primary myoblasts (the immediate progeny of satellite cells) quickly and dramatically downregulate telomerase activity. This work thus suggests that satellite cells, and early transient myoblasts, may be more promising therapeutic candidates for regenerative medicine than traditionally utilized myoblast cultures. Muscle atrophy accompanies human aging, and satellite cells endogenous to aged muscle can be triggered to regenerate old tissue by exogenous molecular cues. Therefore, we also examined whether these aged muscle stem cells would produce tissue that is “young” with respect to telomere maintenance. Interestingly, this work shows that the telomerase activity in muscle stem cells is largely retained into old age wintin inbred “long” telomere mice and in wild‐derived short telomere mouse strains, and that age‐specific telomere shortening is undetectable in the old differentiated muscle fibers of either strain. Summarily, this work establishes that young and old muscle stem cells, but not necessarily their progeny, myoblasts, are likely to produce tissue with normal telomere maintenance when used in molecular and regenerative medicine approaches for tissue repair. © 2009 American Institute of Chemical Engineers Biotechnol. Prog. , 2009
Broadband high-gain 60 GHz antenna array

The design, fabrication and characterization of a 2×8 patch antenna array operating in the IEEE 802.11ad frequency band (57-66 GHz) is presented. The design is based on two-layer structures, where the radiating patches placed on top substrate are fed by conductor backed coplanar waveguide (CPW)-fed loop slots, which are placed on the bottom substrate. The top layer is formed by using a low-cost pyrex (εr = 4.9, tani = 0.01) substrate of 500μm thickness. The pyrex is then etched away to a thickness of 100μm, where 400μm of air volume is formed underneath. This approach does not only benefit from the low-cost feature of pyrex but also exploits the low-loss nature of air. The thin layer of pyrex is solely used for mechanical support for the radiating patches while the air provides good RF-environment for the array. The bottom substrate housing the CPW feed network is an RF-compatible and microfabrication friendly quartz (εr = 3.9, tanδ = 0.0002) of 525μm thickness. The simulations indicate a good maximum realized gain of 19.3 dBi of which variation over ~ 17% bandwidth is relatively constant changing from 17-19.3 dBi.
Applications of Petri Nets in Manufacturing systems; Modeling, Control, and Performance Analysis [Book review]

are discussed in these chapters: model-reference and self-tuning. Design and global convergence for self-tuning, one step look ahead adaptive controllers, and adaptive multistep predictive control algorithms are derived. The problem of singularity is tackled by the introduction of dither signal into the input. Throughout the book, the problems are not given at the end of each chapter, but rather are distributed within the text wherever they illuminate certain aspects of the topics which are being discussed. This causes the reader to be actively involved in the process of exploration into various ideas associated with the problems.
Shape Description with a Space-Variant Sensor: Algorithms for Scan-Path, Fusion, and Convergence Over Multiple Scans

The authors discuss three algorithms related to the blending of a single scene from multiple frames acquired from a space-variant sensor. Given a series of space-variant contour-based scenes with different fixation points, they show how to fuse these into a single multiscan view, which incorporates the information present in the individual scans. They demonstrate an (attentional) algorithm which recursively examines the current knowledge of the scene in order best to choose the next fixation point in terms of focusing attention on regions of maximum boundary curvature. They discuss a simple metric for evaluating convergence over a scan path. This may be used to compare the performance of various attentional algorithms. They discuss their work in light of both machine and biological vision. >
THE DISCRETE ADJOINT METHOD FOR LARGE-SCALE OPTIMIZATION PROBLEMS WITH LINEAR TIME-DEPENDENT PDE CONSTRAINTS

We discuss the application of the discrete adjoint method to large-scale distributed parameterestimation and sensitivity analysis problems that are constrained by linear time-dependent PDEs. The PDEs are solved using an arbitrary-order linear multistep or Runge-Kutta method, making the resulting procedures for the computation of the action of the sensitivity matrix and of the Hessian well-suited to situations where the forward problem needs to be solved to high accuracy. These procedures will depend on the time-stepping method being used and we discuss their implementation in detail. Adjoint linear multistep methods are seen to be equivalent to the corresponding forward schemes apart from the handling of the source terms, and for adjoint Runge-Kutta methods we give a simple argument to show that their order of accuracy is the same as that of the corresponding forward methods. This property is illustrated with a numerical example. The approach used here can easily be adapted to nonlinear PDEs solved using other types of time-stepping methods.
Blood compatibility of PEO grafted polyurethane and HEMA/styrene block copolymer surfaces.

HEMA/styrene (HEMA/STY) block copolymers and poly(ethylene oxide) 4,000 M.W. (PEO4K) grafted Biomer (B-PEO4K) surfaces have been synthesized, characterized, and evaluated as blood-contacting materials. These surfaces have demonstrated improved blood compatibility, compared to Biomer, in in vitro and ex vivo experiments. Biomer vascular grafts (6 mm I.D. 7 cm in length) were fabricated by a dip coating process. The luminal surface was modified either with PEO grafting, HEMA/STY coating, or Biomer coating (control). These surface-modified grafts were implanted in the abdominal aortas of dogs and evaluated for graft patency and protein adsorption. Surface protein layer thickness was measured by transmission electron microscopy (TEM). B-PEO4K and Biomer showed thick multilayers of adsorbed proteins (1000-2000 A) after 3 weeks to 1 month implantation. In contrast, HEMA/STY only showed a monolayer protein thickness (less than 200 A), even after 3 months. Visualization of adsorbed plasma proteins (albumin, IgG, and fibrinogen) was performed with scanning electron microscopy (SEM)/TEM using an immunogold double antibody technique. The pattern of protein distribution showed high concentrations of fibrinogen and IgG, and less albumin adsorbed onto Biomer and B-PEO4K. In contrast, HEMA/STY showed a patchy protein distribution pattern with high concentrations of albumin and IgG, and relatively less fibrinogen. Adsorbed monolayer patterns showed improved compatibility over multilayered proteins. The Biomer and B-PEO4K grafts occluded within 1 month, while HEMA/STY grafts were patent for over 3 months. The thin and stable adsorbed protein layer on HEMA/STY surfaces may be associated with the microdomain structures of the surface, and will play an important role in long-term in vivo blood compatibility. This manuscript will evaluate the long-term in vivo performance of these polymers, analyze the extent of protein adsorption onto the surfaces, and correlate protein layer thickness to the thrombogenicity of the polymer surfaces.
Dietary self-selection for organic acids by the piglet

Two feeding trials using 48 weaned crossbred piglets each were carried out to determine the effect of acidifying diets with potassium diformate (K-diformate), formic or sorbic acid on dietary preferences in piglets. In Exp. 1 two reference groups were fed either an unacidified diet or a diet containing 2.4% of K-diformate with no choice for selection. Furthermore, piglets in choice group 1 and 2 had the choice between an unacidified diet and a diet supplemented with 1.2 and 2.4% K-diformate, respectively. In Exp. 2, animals of three reference groups received exclusively an unacidified diet or diets supplemented with 1.2% formic acid or 1.2% sorbic acid, respectively. The animals of the choice groups had the choice between an unacidified diet and diets with 1.2% formic acid or 1.2% sorbic acid, respectively. In Exp. 1 average daily feed intake, daily gain and feed conversion ratio were 751 g, 458 g and 1.64 kg/kg, respectively, with no significant differences between treatments. In both choice feeding groups animals chose the diets on offer at random (each around 50%). In Exp. 2 growth and feed intake were not affected by the treatment, but feed conversion ratio was enhanced due to the 1.2% formic acid supplementation. Animals of both organic acid choice groups showed a significant preference for the unacidified diets in each experimental week. The formic acid and sorbic acid diets represented on average only 13.5% and 23.5% of the total feed intake. The present results demonstrate that the inclusion of 1.2% sorbic or formic acid or 2.4% of K-diformate in piglet diets has no negative impact on feed intake, but in a situation of choice feeding, piglets will refuse diets acidified with 1.2% formic or sorbic acid, presumably because of negative taste cues. Acidifying the diets with varying amounts of a K-diformate had no effect on dietary preferences of piglets.
Vertebrate MicroRNA Genes

MicroRNAs (miRNAs) are an abundant class of ∼22-nucleotide (nt) noncoding RNAs, some of which are known to control the expression of other genes at the posttranscriptional level ([1–4][1]). We developed a computational procedure (MiRscan) to identify miRNA genes ([5][2]) and apply it here to
Constant-Frequency Magnetically Controlled Universal Ballast With SoS Compliance for TL5 Fluorescent Lamps

This paper presents the development of a universal electronic ballast for TL5 lamps. The intent is to efficiently operate the maximum number of TL5 lamps with different power ratings at nominal power, using a resonant variable inductance, provided by a magnetic regulator, while maintaining the switching frequency constant. A microcontroller and additional digital circuitry are used to command a dc-dc buck converter to supply the necessary dc control current to the magnetic regulator and to regulate the switching frequency of the half-bridge resonant inverter that supplies the lamp. The selection of the resonant capacitance is done in order to comply with the SoS limits established for each lamp. Experimental results with lamps ranging from 14 to 49 W, operating with high efficiency and high output, are presented in this paper.
Pieces of Mind

Many people accept that chimpanzees, dolphins, and some other animals can think and feel. But these cases are just the tip of a growing iceberg. If biologists are right, fruit flies and plants make decisions, worms and honeybees can be trained, bacteria communicate linguistically, and neurons have preferences. Just how far does cognition go? This book is the first to critically consider this question from the perspective of the entire range of new ascriptions of psychological capacities throughout biology. It is also the first to consider the role of mathematical models and other quantitative forms of evidence in prompting and supporting the new ascriptions. It defends a default literal interpretation of psychological terms across biological domains. It also considers the implications of the literal view for efforts to explain the mind’s place in nature and for traditional ways of distinguishing the superior moral status of humans relative to other living beings.
Dual-frequency patch antennas

Dual-frequency patch antennas may provide an alternative to large-bandwidth planar antennas, in applications in which large bandwidth is really needed for operating at two separate transmit-receive bands. When the two operating frequencies are far apart, a dual-frequency patch structure can be conceived to avoid the use of separate antennas. In this paper, a critical overview of possible solutions for dual-frequency patch antennas is presented, and future perspectives are outlined. Geometries are discussed in particular.
A 1 mm Pitch $80 \times 80$ Channel 322 Hz Frame-Rate Multitouch Distribution Sensor With Two-Step Dual-Mode Capacitance Scan

A 1 mm pitch 80 X 80 channel 322 Hz framerate capacitive multitouch distribution sensor has been developed. High-resolution multiple touch points are detected including touch-strength distribution around them. A two-step dual-mode capacitance scan scheme is proposed, where self- and mutual-capacitance measurements are hierarchically performed in two steps to increase the frame scan rate that is otherwise reduced due to high resolution. 160 row-and-column dedicated parallel ADCs further increase the scan rate. A time-domain counter-based slope ADC suppresses power and area penalty for the parallel ADC approach. A signal attenuation due to the sensor capacitance reduction in the high resolution is compensated by thorough noise-reduction techniques in the sensor analog frontend (AFE). A prototype in 0.35 μm CMOS demonstrates 41 dB signal-to-noise ratio (SNR) with >5× tighter sensor-channel pitch, >10× faster touch-point scan, >10× and >4× higher energy and area efficiency to the state-of-the-art touch distribution sensors.
Structure of Fam20A reveals a pseudokinase featuring a unique disulfide pattern and inverted ATP-binding

Mutations in FAM20A cause tooth enamel defects known as Amelogenesis Imperfecta (AI) and renal calcification. We previously showed that Fam20A is a secretory pathway pseudokinase and allosterically activates the physiological casein kinase Fam20C to phosphorylate secreted proteins important for biomineralization (Cui et al., 2015). Here we report the nucleotide-free and ATP-bound structures of Fam20A. Fam20A exhibits a distinct disulfide bond pattern mediated by a unique insertion region. Loss of this insertion due to abnormal mRNA splicing interferes with the structure and function of Fam20A, resulting in AI. Fam20A binds ATP in the absence of divalent cations, and strikingly, ATP is bound in an inverted orientation compared to other kinases. Fam20A forms a dimer in the crystal, and residues in the dimer interface are critical for Fam20C activation. Together, these results provide structural insights into the function of Fam20A and shed light on the mechanism by which Fam20A mutations cause disease. DOI: http://dx.doi. org/10.7554/eLife.23990. 001