Miracle-dz/UniFAR-FTUs huggingface dataset:
Histologic, Immunohistochemical, and Clinical Features of 27 Mammary Tumors in 18 Male Dogs

Twenty-seven mammary tumors from 18 male (3 intact, 15 neutered) dogs were collected. The average age at diagnosis was 9.2 years (range, 2–14 years). Seven of the dogs were Cocker Spaniels. Five dogs had multiple mammary tumors. All tumors were benign. Twenty-six were simple adenomas with mixed acinar and papillary patterns. The acinar pattern was predominant in 17 cases. One adenoma was complex with a prominent myoepithelial component. The myoepithelial component of 25 of the 25 tumors was immunohistochemically positive for calponin and p63. In the cases for which relevant clinical information was available, there was no reported history of obesity, testicular tumors, or sex hormone therapy. Surgery was the only reported treatment for these tumors. Only 1 dog was reported to have developed an additional mammary tumor. None of the dogs for which case outcome was known died or was euthanatized as a result of mammary tumor. Although uncommon, mammary tumors do occur in male dogs. Although mammary tumors may be quite cellular, the presence of an intact myoepithelium, which can be demonstrated with immunohistochemistry for calponin and p63, indicates benignancy, as the clinical behavior documents.
Live-cell monitoring of tyrosine phosphorylation in focal adhesions following microtubule disruption

Tyrosine phosphorylation of focal adhesion components is involved in the regulation of focal adhesion formation and turnover, yet the underlying molecular mechanisms are still poorly defined. In the present study, we have used quantitative fluorescence microscopy to investigate the dynamic relationships between the incorporation of new components into growing focal adhesions and tyrosine phosphorylation of these sites. For this purpose, a new approach for monitoring phosphotyrosine levels in live cells was developed, based on a `phosphotyrosine reporter' consisting of yellow fluorescent protein fused to two consecutive phosphotyrosine-binding Src-homology 2 (SH2)-domains derived from pp60c-Src. This YFP-dSH2 localized to cell-matrix adhesions and its intensity was linearly correlated with that of an anti-phosphotyrosine antibody labeling. The differential increase in vinculin and phosphotyrosine levels was examined in live cells by two-color time-lapse movies of CFP-vinculin and YFP-dSH2. In this study, focal adhesion growth was triggered by microtubule disruption, which was previously shown to stimulate focal adhesion development by inducing cellular contraction. We show here that, 2 minutes after addition of the microtubule-disrupting drug nocodazole, the local densities of the focal adhesion-associated proteins vinculin, paxillin and focal adhesion kinase (FAK) are significantly elevated and the focal adhesion area is increased, whereas elevation in tyrosine phosphorylation inside the growing adhesions occurs only a few minutes later. Phosphotyrosine and FAK density reach their maximum levels after 10 minutes of treatment, whereas vinculin and paxillin levels as well as focal adhesion size continue to grow, reaching a plateau at about 30 minutes. Our findings suggest that protein recruitment and growth of focal adhesions are an immediate and direct result of increased contractility induced by microtubule disruption, whereas tyrosine phosphorylation is activated later.
A Multi-Sectoral Approach to the U.S. Great Depression

We document sectoral differences in changes in output, hours worked, prices and nominal wages in the US during the Great Depression. We explore whether contractionary monetary shocks combined with different degrees of nominal wage frictions across sectors are consistent with both sectoral as well as aggregate facts. To do so, we construct a two-sector model where goods from each sector are used as intermediates to produce the sectoral goods that in turn produce final output. One sector is assumed to have flexible nominal wages, while nominal wages in the other sector are set using Taylor contracts. We calibrate the model to the U.S. economy in 1929, and then feed in monetary shocks estimated from the data. We find that while the model can qualitatively replicate the key sectoral facts, it can account for less than a third of the decline in aggregate output. This decline in output is roughly half as large as the one implied by a one-sector model. Alternatively, if wages are set using Calvo-type contracts the decline in output is even smaller.
Identification of differentially methylated loci using wavelet-based functional mixed models

MOTIVATION DNA methylation is a key epigenetic modification that can modulate gene expression. Over the past decade, a lot of studies have focused on profiling DNA methylation and investigating its alterations in complex diseases such as cancer. While early studies were mostly restricted to CpG islands or promoter regions, recent findings indicate that many of important DNA methylation changes can occur in other regions and DNA methylation needs to be examined on a genome-wide scale. In this article, we apply the wavelet-based functional mixed model methodology to analyze the high-throughput methylation data for identifying differentially methylated loci across the genome. Contrary to many commonly-used methods that model probes independently, this framework accommodates spatial correlations across the genome through basis function modeling as well as correlations between samples through functional random effects, which allows it to be applied to many different settings and potentially leads to more power in detection of differential methylation. RESULTS We applied this framework to three different high-dimensional methylation data sets (CpG Shore data, THREE data and NIH Roadmap Epigenomics data), studied previously in other works. A simulation study based on CpG Shore data suggested that in terms of detection of differentially methylated loci, this modeling approach using wavelets outperforms analogous approaches modeling the loci as independent. For the THREE data, the method suggests newly detected regions of differential methylation, which were not reported in the original study. AVAILABILITY AND IMPLEMENTATION Automated software called WFMM is available at https://biostatistics.mdanderson.org/SoftwareDownload CpG Shore data is available at http://rafalab.dfci. harvard.edu NIH Roadmap Epigenomics data is available at http://compbio.mit. edu/roadmap SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT jefmorris@mdanderson.org.
Reforming the local public sector: economics and politics in privatization of water and solid waste

Several empirical studies have analyzed the factors that influence local privatization. We examine the influence of transaction costs and political factors on local governments’ choices through new variables. We consider two relevant services accounting for different amounts of transaction costs: water and solid waste delivery. Our results show that privatization is less common for water, which has higher transaction costs. Furthermore, we find that municipalities with a conservative ruling party privatize more often regardless of the ideological orientation of the constituency. Finally, we find that intermunicipal cooperation may be a suitable organizational form for some municipalities.
Do junior doctors feel they are prepared for hospital practice? A study of graduates from traditional and non‐traditional medical schools

A valid and reliable questionnaire was developed which assesses eight subscales relating to key areas of medical hospital‐based work. This was used to evaluate junior doctors' perceptions of the adequacy of their undergraduate medical training to prepare them for hospital practice. Data from 139 (60%) first‐year doctors (interns) showed that graduates from the problem‐based medical school rated their undergraduate preparation more highly than traditional medical school graduates in preparing them for practice in the areas of interpersonal skills, confidence, collaboration with other health care workers, preventive care, holistic care and self‐directed learning. These findings persisted when ratings were adjusted for the effects of age and gender. There were no differences between the intern groups for patient management and understanding science. This research suggests that educational experiences in different undergraduate medical courses are important in preparing doctors for their early working life.
Wireless Sensor Networks and Computational Geometry

Wireless Sensor Networks Due to its potential applications in various situations such as battle eld, emergency relief, environment monitoring, and so on, wireless sensor networks [50, 75, 118, 130] have recently emerged as a premier research topic. Sensor networks consist of a set of sensor nodes which are spread over a geographical area. These nodes are able to perform processing as well as sensing and are additionally capable of communicating with each other by means of a wireless ad hoc network. With coordination among these sensor nodes, the network together will achieve a larger sensing task both in urban environments and in inhospitable terrain. The sheer numbers of these sensors and the expected dynamics in these environments present unique challenges in the design of wireless sensor networks. Many excellent researches have been conducted to study problems in this new eld [50, 69, 75, 118, 119, 130]. In this chapter, we consider a wireless sensor network consisting of a set V of n wireless sensor nodes distributed in a two-dimensional plane. Each wireless sensor node has an omni-directional antenna. This is attractive because a single transmission of a node can be received by many nodes within its vicinity which, we assume, is a disk centered at the node. We call the radius of this disk the transmission range of this sensor node. In other words, node v can receive the signal from node u if node v is within the transmission range of the sender u. Otherwise, two nodes communicate through multi-hop wireless links by using intermediate nodes to relay the message. Consequently, each node in the sensor network also acts as a router, forwarding data packets for other nodes. By a proper scaling, we assume that all nodes have the maximum transmission range equal to one unit. These wireless sensor nodes de ne a unit disk graph UDG(V ) in which there is an edge between two nodes if and only if their Euclidean distance is at most one. In addition, we assume that each node has a low-power Global Position System (GPS) receiver, which provides the position information of the node itself. If GPS is not available, the distance between neighboring nodes can be estimated on the basis of incoming signal strengths. Relative co-ordinates of neighboring nodes can be obtained by exchanging such information between neighbors [26]. With the position information, we can apply computational geometry techniques to solve some challenging questions in sensor networks.
Dolutegravir in breast milk and maternal and infant plasma during breastfeeding.

The integrase inhibitor dolutegravir (DTG) is a new effective first-line antiretroviral agent for treatment-naive HIV-positive individuals with a variety of baseline characteristics [1–5]. Because of its effectiveness, good tolerability, limited drug–drug interactions, and highresistance barrier, DTG is also suggested as possible treatment option in the resource-limited setting [6], where WHO recommends exclusive breastfeeding for infants of HIV-positive mothers, as formula feeding is associated with high infant mortality [7]. However, to date, no pharmacokinetic and safety data of DTG from lactating women and their breastfed infants are available. Here, we present the first case of DTG transfer into breast milk and the breastfed infant.
The Nested Recursive Two-Level Factorization Method for Nine-Point Difference Matrices

Nested recursive two-level factorization methods for nine-point difference matrices are analyzed. Somewhat similar in construction to multilevel methods for finite element matrices, these methods use recursive red-black orderings of the meshes, approximating the nine-point stencils by five-point ones in the red points and then forming the reduced system explicitly. Because this Schur complement is again a nine-point matrix (on a skew grid this time), the process of approximating and factorizing can be applied anew. Progressing until a sufficiently coarse grid has been reached, this procedure gives a multilevel preconditioner for the original matrix. Solving the levels in V-cycle order will not give an optimal order method (that is, with a total work proportional to the number of unknowns), but we show that using certain combinations of V-cycles and W-cycles will give methods of both optimal order of numbers of iterations and computational complexity.Since all systems to be solved during a preconditioner s.
Superoxide production by phagocytic leukocytes

Mononuclear phagocytic leukocytes, as well as polymorphonuclear leukocytes, produce and release superoxide at rest, and this is stimulated by phagocytosis. Of the mouse monocytic cells studied, alveolar macrophages released the largest amounts of superoxide during phagocytosis, followed by normal peritoneal macrophages. Casein- elicited and "activated" macrophages released smaller quantities. In the guinea pig, polymorphonuclear leukocytes and casein-elicited macrophages were shown to release superoxide during phagocytosis whereas alveolar macrophages did not. Superoxide release accounted for only a small fraction of the respiratory burst of phagocytosis in all but the normal mouse peritoneal macrophage, the guinea pig polymorphonuclear leukocyte, and probably the mouse alveolar macrophage. There are obviously considerable species differences in O2- release by various leukocytes that might reflect both the production and/or destruction (e.g. by dismutase) of that substance.
A novel global optimization technique for high dimensional functions

Several types of line search methods are documented in the literature and are well known for unconstraint optimization problems. This paper proposes a modified line search method, which makes use of partial derivatives and restarts the search process after a given number of iterations by modifying the boundaries based on the best solution obtained at the previous iteration (or set of iterations). Using several high‐dimensional benchmark functions, we illustrate that the proposed line search restart (LSRS) approach is very suitable for high‐dimensional global optimization problems. Performance of the proposed algorithm is compared with two popular global optimization approaches, namely, genetic algorithm and particle swarm optimization method. Empirical results for up to 2000 dimensions clearly illustrate that the proposed approach performs very well for the tested high‐dimensional functions. © 2009 Wiley Periodicals, Inc.
FTUNSHADES2: A novel platform for early evaluation of robustness against SEE

Large digital integrated circuits designed to solve space applications, have to be designed following standards that recommend to include hardening techniques against Single Event Phenomena caused by harsh radiation environments. It is specifically important in the case of modern deep-submicron technologies. Single Event Effects are phenomena related to the effects of radiation when ionizing particles hit the surface of semiconductors in certain critical areas, where the consequences are mainly data corruption or unexpected behavior with no permanent damage. Fault injection studies are a valuable methodology to evaluate the robustness of the circuit mainly in the early stages of the design. This paper introduces the second generation of the emulation-based fault injection platform FTUNSHADES supported by the European Space Agency, where new features have been included to fulfill with the demands of a growing community of users.
LIPS

This article presents a Light Intensity--based Positioning System (LIPS) for indoor environments. The system uses off-the-shelf light-emitting diode lamps as signal sources and light sensors as signal receivers. The design is inspired by the observation that a light sensor has deterministic sensitivity to both the distance and incident angle of a light signal, an under-utilized feature of photodiodes now widely found on mobile devices. We develop a stable and accurate light intensity model to capture the phenomenon, based on which a new positioning principle, Multi-Face Light Positioning, is established that uses three collocated sensors to uniquely determine the receiver’s position, assuming merely a single source of light. We have implemented a prototype on both dedicated embedded systems and smartphones. Experimental results show average positioning accuracy within 0.4m across different environments, with high stability against interferences from obstacles, ambient lights, temperature variation, and so on.
Nox-2-Mediated Phenotype Loss of Hippocampal Parvalbumin Interneurons Might Contribute to Postoperative Cognitive Decline in Aging Mice

Postoperative cognitive decline (POCD) is a common complication following anesthesia and surgery, especially in elderly patients; however, the precise mechanisms of POCD remain unclear. Here, we investigated whether nicotinamide adenine dinucleotide phosphate (NADPH) oxidase mediated-abnormalities in parvalbumin (PV) interneurons play an important role in the pathophysiology of POCD. The animal model was established using isoflurane anesthesia and exploratory laparotomy in 16-month-old male C57BL/6 mice. For interventional experiments, mice were chronically treated with the NADPH oxidase inhibitor apocynin (APO). Open field and fear conditioning behavioral tests were performed on day 6 and 7 post-surgery, respectively. In a separate experiment, brain tissue was harvested and subjected to biochemical analysis. Primary hippocampal neurons challenged with lipopolysaccharide (LPS) in vitro were used to investigate the mechanisms underlying the oxidative stress-induced abnormalities in PV interneurons. Our results showed that anesthesia and surgery induced significant hippocampus-dependent memory impairment, which was accompanied by PV interneuron phenotype loss and increased expression of interleukin-1β (IL-1β), markers of oxidative stress and NADPH oxidase 2 (Nox2) in the hippocampus. In addition, LPS exposure increased Nox2 level and decreased the expression of PV and the number of excitatory synapses onto PV interneurons in the primary hippocampal neurons. Notably, treatment with APO reversed these abnormalities. Our study suggests that Nox2-derived reactive oxygen species (ROS) production triggers, at least in part, anesthesia- and surgery-induced hippocampal PV interneuron phenotype loss and consequent cognitive impairment in aging mice.
Anticonvulsant, Anxiolytic, and Sedative Activities of Verbena officinalis

We describe different neuropharmacological effects of Verbena officinalis crude extract (Vo.Cr). Pentylenetetrazole (PTZ)-induced seizures, elevated plus maze, light–dark box (LDB), open field and thiopental-induced sleeping test models were employed to evaluate Vo.Cr actions in mice. Vo.Cr dose-dependently (100–500 mg/Kg) delayed onset time of myoclonic jerks and tonic-clonic seizures, while decreased duration of tonic-clonic seizures (P < 0.05, P < 0.001 vs. saline group). Vo.Cr at 100 and 300–500 mg/Kg doses reduced animals’ mortality in PTZ-induced seizures test to 75 and 0%, respectively. Vo.Cr (50–300 mg/Kg) significantly increased time spent and number of entries into open arms, while decreased time spent and number of entries into closed arms (P < 0.05, P < 0.01, P < 0.001 vs. saline group), measured in elevated plus maze. Vo.Cr (50–300 mg/Kg) increased time spent in light compartment, while decreased time spent in dark compartment (P < 0.01, P < 0.001 vs. saline group) in LDB, like caused by diazepam. In open field test, Vo.Cr decreased number of ambulations and rearings frequencies, while increased the number of central squares crossings. In thiopental-induced sleeping test, Vo.Cr (50–300 mg/Kg) decreased onset time of sleep, while increased the duration of sleep (P < 0.05, P < 0.01, P < 0.001 vs. saline group). These results indicate that Verbena officinalis possess anticonvulsant, anxiolytic and sedative activities, which provides scientific background for its medicinal application in various neurological ailments, such as epilepsy, anxiety, and insomnia.
A Holistic Approach for Recognition of Complete Urdu Ligatures Using Hidden Markov Models

Optical Character Recognition (OCR) is one of the continuously explored problems. Presently, commercial character recognizers are available reporting near to 100% recognition rates on text in a number of scripts. Despite these advancements, OCR systems however, have yet to mature for cursive scripts like Urdu. This study presents a holistic technique for recognition of Urdu text in Nastaliq font using "complete" ligatures as recognition units. The term "complete" refers to a partial word including its main body and secondary components (dots and diacritic marks). Discrete Wavelet Transform (DWT) is employed as feature extractor while a separate Hidden Markov Model (HMM) is trained for each ligature considered in our study. More than 2000 frequently used unique Urdu ligatures from the standard CLE (Center of Language Engineering) dataset are considered in our evaluations. The system reads a promising accuracy of 88.87% on more than 10,000 partial words.
Cohomology of Filippov algebras and an analogue of Whitehead's lemma

We show that two cohomological properties of semisimple Lie algebras also hold for Filippov (n-Lie) algebras, namely, that semisimple n-Lie algebras do not admit non-trivial central extensions and that they are rigid i.e., cannot be deformed in Gerstenhaber sense. This result is the analogue of Whitehead's Lemma for Filippov algebras. A few comments about the n-Leibniz algebras case are made at the end.
Propagation of Surface Cracks Under Cyclic Loading

In this work we propose to predict the evolution of the semi-elliptical surface crack geometry in fatigue, contained in thick plates and in thick tubes under internal pressure. The use of the global approach, based on the minimization of the potential energy, permits us to evaluate the energy release rate, the global stress intensity factor and to follow the evolution of the two half-axes of the crack during its propagation, this without the recourse to use a propagation law. A count code based on a three dimensional finite element method has been made by us. The energy release rate so calculated from experimental data permits us to predict with a very high precision the evolution of the crack geometry during its evolution under two types of loading.