Miracle-dz/UniFAR-FTUs huggingface dataset:
ŌvSim: a Simulation of the Population Dynamics of Mammalian Ovarian Follicles

No two ovaries are alike, and indeed, the same ovary can change its architecture from day to day. This is because ovarian follicles are present in different numbers, positions, and states of maturation throughout reproductive life. All possible developmental states of follicles can be represented at any time, along with follicles that have committed to death (termed follicle atresia). Static histological and whole-mount imaging approaches allow snapshots of what is occurring within ovaries, but our views of dynamic follicle growth and death have been limited to these tools. We present a simple Markov chain model of the complex mouse ovary, called “ŌvSim”. In the model, follicles can exist in one of three Markov states with stationary probabilities, Hold (growth arrest), Grow, and Die. The probability that individual primordial follicles can growth activate daily, the fraction of granulosa cells that survive as follicles grow, and the probability that individual follicles can commit to atresia daily are user definable parameters. When the probability of daily growth activation is stationary at 0.005, the probability of atresia for all follicles is near 0.1, and the probability of granulosa cell survival is modeled around 0.88, ŌvSim simulates the growth and fate of each of the approximately 3000 postpubertal mouse ovarian follicles in a fashion that approximates actual biological measurements (e.g., follicle counts). ŌvSim thus offers a starting platform to simulate mammalian ovaries and to explore factors that might impact follicle development and global organ function. Author Summary ŌvSim is a computer simulation of the dynamic growth of mouse ovarian follicles. The program is offered as the beginning of a research and teaching platform to model asynchronous follicle growth and survival or death.
Transparent surface modeling from a pair of polarization images

We propose a method for measuring surface shapes of transparent objects by using a polarizing filter. Generally, the light reflected from an object is partially polarized. The degree of polarization depends upon the incident angle, which, in turn, depends upon the surface normal. Therefore, we can obtain surface normals of objects by observing the degree of polarization at each surface point. Unfortunately, the correspondence between the degree of polarization and the surface normal is not one to one. Hence, to obtain the correct surface normal, we have to solve the ambiguity problem. In this paper, we introduce a method to solve the ambiguity by comparing the polarization data in two objects, i.e., normal position and tilted with small angle position. We also discuss the geometrical features of the object surface and propose a method for matching two sets of polarization data at identical points on the object surface.
Choix de portefeuille : clauses de garantie et attitude face au risque

La recente crise financiere a remis l’accent sur deux questions importantes en finance : 1) Quelles sont les formes de garantie qu’un investisseur est en droit d’exiger, du moins a court terme ? 2) Quels sont les determinants de choix de l’investisseur face au risque? Pour apporter un nouvel eclairage sur ces deux problemes, cette these est organisee de la maniere suivante: Dans la premiere partie, nous developpons des modeles d’assurance de portefeuille qui sont des extensions de la methode CPPI standard. Dans ce cadre nous proposons d’introduire et d’analyser des nouvelles methodes de gestion dynamique, de type CPPI, ou le risque est controle via des conditions de type « quantile local » et d’ « expected shortfall». Dans la deuxieme partie, nous traitons des consequences du comportement d’un investisseur non conforme au critere de l’utilite esperee, en considerant le cadre de l’utilite dependante du rang, notamment le cas de l’utilite anticipee de Quiggin et celui de la theorie des perspectives cumulees de Kahneman et Tversky. Nous montrons comment la prise en compte de telles attitudes face au risque modifient profondement la composition du portefeuille optimal par rapport au cas standard.
Reprogramming over Low Power Link Layer in Wireless Sensor Networks

Reprogramming over the air is important for maintaining a wireless sensor network. Traditional reprogramming approaches assume always-on link layers. Given the energy limitation of sensor nodes, always-on link layers are often not desired for most sensor network applications. In this paper, we propose ROLP, a novel reprogramming protocol built on a widely used low power link layer in wireless sensor networks. ROLP employs an efficient control packets self-suppression scheme for reliable data transmission. ROLP also employs an adaptively falling asleep scheme based on the neighbor information to reduce the energy consumption. We implement ROLP based on TinyOS and evaluate its performance in two different indoor networks. Compared with the standard reprogramming protocol in TinyOS, ROLP is able to reduce the radio-on time by 57.6% and 39.0% in the two networks. Since radio operations cost most of the energy, these reductions save significant amount of energy and prolong the lifetime of a wireless sensor network.
Menstrual cycle-dependent changes of Toll-like receptors in endometrium.

BACKGROUND Rapid innate immune defences against infection usually involve the recognition of invading pathogens by specific pattern recognition receptors recently attributed to the family of Toll-like receptors (TLRs). Reports from our laboratory and others have demonstrated the existence of TLRs 1-6 in the female reproductive tract. However, little has been done to identify TLRs 7-10 in the female reproductive tract, particularly in the uterus. Also little information exists regarding variation in TLRs in the female reproductive tract during the menstrual cycle. METHOD The distribution of TLR7-10 protein was detected by immunostaining in timed endometrial biopsies from normal women. RT-PCR was used to show the existence of TLR1-10 genes in endometrial tissue and real-time PCR analysis to investigate the relative expression of these genes during the menstrual cycle in normal human endometrium. RESULTS TLR7-10 proteins were detected in endometrial epithelium and stroma. TLR1-10 genes were expressed in human endometrial tissue, and the mean relative expression of TLR2-6, 9 and 10 genes was significantly higher during the secretory phase compared with other phases of the menstrual cycle. CONCLUSIONS TLR7-10 localization is not limited to endometrial epithelium but is also present in the stroma of the endometrial tissue. Endometrial TLR2-6, 9 and 10 genes are cyclically expressed during the menstrual cycle.
Multivariate Gaussian Document Representation from Word Embeddings for Text Categorization

Recently, there has been a lot of activity in learning distributed representations of words in vector spaces. Although there are models capable of learning high-quality distributed representations of words, how to generate vector representations of the same quality for phrases or documents still remains a challenge. In this paper, we propose to model each document as a multivariate Gaussian distribution based on the distributed representations of its words. We then measure the similarity between two documents based on the similarity of their distributions. Experiments on eight standard text categorization datasets demonstrate the effectiveness of the proposed approach in comparison with state-of-the-art methods.
Development of Situational Requirements Engineering Processes: A Process Factory Approach

The Software Product Line (SPL) approach is a paradigm for systematic reuse of software products, and a Software Factory is a SPL aimed at the industrialization of software development. Based on the notion that a software/RE process can be developed via an engineering process (much akin to engineering other types of software), this research aims to provide a feature-based RE process factory to develop RE processes based on the characteristics of the project at hand (project situation). In our approach, the project situation is modeled as the problem domain through using the i* modeling language (resulting in a situation model). A feature model can encapsulate all the features in an SPL; therefore, the abundant riches of the RE field -- results of decades of research -- have been explored for extracting the variations and commonalities among existing RE processes, the results of which are represented in the form of a feature model, considered as a model of the solution domain. In order to demonstrate the validity of the proposed feature model, it has been compared against RE-related activities found in prominent software development methodologies. A mapping for translating the situation model to the RE process feature model is proposed with the specific aim of promoting traceability and rationality in the selection of RE process features. The efficacy of the approach is demonstrated through an RE process development example.
A randomized trial comparing intensive and passive education in patients with diabetes mellitus.

BACKGROUND Patient education is a cornerstone of treatment in diabetes mellitus, but there is not unanimity of opinion as to how it should be delivered. OBJECTIVE To determine whether a single, intensive group educational program would improve glycosylated hemoglobin (HbA(1c)) levels when compared with passive education. METHODS A total of 106 patients with HbA(1c) levels greater than 8.5% were randomized to either an intensive (n = 50) or a passive education (n = 56) group. The intensive education group received 3.5 days of a structured curriculum involving a physician, nurse, nutritionist, pharmacist, exercise physiologist, and a social worker. The passive education group received material sent by mail every 3 months providing basic information on topics related to diabetes management. Patients continued care with their diabetes care provider during the study period. Levels of HbA(1c) were measured at baseline and 3, 6, and 12 months after randomization. A matched control group of individuals who declined participation also had HbA(1c) levels measured at baseline and 12 months. RESULTS Mean +/- SD HbA(1c) levels fell significantly (P<.001) from baseline (9.9% +/- 1.3%) in both the intensive (-2.0%) and passive (-1.9%) education groups at 12 months, and there was no difference between the groups at any evaluation time. Both groups had significantly greater decline (P<.03) in HbA(1c) levels than a matched control group (-1.2%) with similar baseline HbA(1c) levels that did not receive education. CONCLUSIONS Patients with elevated HbA(1c) levels who were receptive to education had substantial improvement in HbA(1c) levels after receiving an educational intervention. In this population, intensive or passive methods of delivering patient education seemed to have similar effect on improving glycemic control.
Task Allocation and Migration Algorithm for Temperature-Constrained Real-Time Multi-Core Systems

Temperature rise will affect the stability and performance of multi-core processors. A temperature-aware task scheduling algorithm for real-time multi-core systems, called LTEDF (Low Thermal Early Deadline First), is proposed in this paper. In LTEDF, a HCNF ( History Coolest Neighborhood First) task allocation algorithm is employed to balance the loads. When some cores are thermally saturated, task migration is performed to alleviate thermal saturation to get more uniform power density map. A thermal aware multi-core scheduling simulator(TAMSS) based on Hot Spot thermal model is implemented. TAMSS simulation results show that LTEDF algorithm can not only meet real-time guarantee, but also minimize the thermal penalty. Moreover, it can create a more uniform power density map than other thermal-aware algorithms, and significantly reduce thread migration frequency.
Performance bounds of concatenated polar coding schemes

A concatenated coding scheme using a polarization transformation followed by outer sub-codes is analyzed. Achievable error exponents and upper bounds on the error rate are derived. The first bound is obtained using outer codes which are typical linear codes from the ensemble of parity check matrices whose elements are chosen independently and uniformly. As a byproduct of this bound, it determines the required rate split of the total rate to the rates of the outer codes. A lower bound on the error exponent that holds for all BMS channels with a given capacity is then derived. Improved bounds and approximations for small blocklength codes are also obtained. The bounds are compared to actual simulation results from the literature.
Leveraging Protocol-Oblivious Forwarding (POF) to Realize NFV-Assisted Mobility Management

In the Internet, to enable emerging network services such as e-Health to be delivered to numerous people anytime and anywhere, mobility management plays an important role. In this work, we leverage the protocol-oblivious forwarding (POF) to design a novel network system that can realize highly-efficient mobility management and overcome the drawbacks of existing approaches. Moreover, we explore the forwarding plane programmability provided by POF to realize dynamic virtual network function (vNF) deployment for traffic adaption. We implement our system and conduct experiments to verify that it functions well for NFV-assisted mobility management and achieves reduced handover latency and enhanced QoE.
The effect of handedness on academic ability: A multivariate linear mixed model approach

In recent years questions have arisen about whether there are any links between handedness and academic abilities as well as other factors. In this study we investigate the effects of gender, writing hand, relative hand skill, and UK region on mathematics and reading test scores by applying a multivariate linear mixed-effects model. A data sample based on 11,847 11-year-old pupils across the UK from the National Child Development Study was considered for the analysis. Our results show that pupils who write with one hand while having better skill with their other hand (i.e., inconsistent writing hand and superior hand) obtained lower test scores in both reading and mathematics than pupils with consistent writing hand and superior hand. Furthermore, we confirm previous findings that degree of relative hand skill has a significant effect on both reading and maths scores and that this association is not linear. We also found higher scores of reading in children from the south of England, and of mathematics in children from the south of England and Scotland, when compared to other UK regions.
Expanding the Design Horizon for Self-Driving Vehicles: Distributing Benefits and Burdens

With over one billion vehicles in the world today, the motorized road vehicle is the pillar of modern society. Since the beginning of the 20th century, the automobile has revolutionized our spaces, practices, cultures, and identities through a complex matrix of technical, financial, economic, political, and social linkages. Visions of automobile use have always shaped its design, manufacture, and production. Now, motorized road transport is set to revolutionize our society once again on a huge scale. Recent technological developments in propulsion, telecommunications, sensing, and in-vehicle computing technology are expanding the range of vehicles? capabilities. A technological convergence is underway, moving towards self-driving vehicle (SDV) technology. These vehicles will utilize computational algorithms, sensors, and communication devices to automatically navigate a variety of environments with limited or no intervention from human drivers.
k-Calling context profiling

Calling context trees are one of the most fundamental data structures for representing the interprocedural control flow of a program, providing valuable information for program understanding and optimization. Nodes of a calling context tree associate performance metrics to whole distinct paths in the call graph starting from the root function. However, no explicit information is provided for detecting short hot sequences of activations, which may be a better optimization target in large modular programs where groups of related functions are reused in many different parts of the code. Furthermore, calling context trees can grow prohibitively large in some scenarios. Another classical approach, called edge profiling, collects performance metrics for caller-callee pairs in the call graph, allowing it to detect hot paths of fixed length one. We study a generalization of edge and context-sensitive profiles by introducing a novel data structure called k-calling context forest (k-CCF). Nodes in a k-CCF associate performance metrics to paths of length at most k that lead to each distinct routine of the program, providing edge profiles for k=1, full context-sensitive profiles for k equal to infinity, as well as any other intermediate point in the spectrum. We study the properties of the k-CCF both theoretically and experimentally on a large suite of prominent Linux applications, showing how to construct it efficiently and discussing its relationships with the calling context tree. Our experiments show that the k-CCF can provide effective space-accuracy tradeoffs for interprocedural contextual profiling, yielding useful clues to the hot spots of a program that may be hidden in a calling context tree and using less space for small values of k, which appear to be the most interesting in practice.
New-Onset Refractory Status Epilepticus with Claustrum Damage: Definition of the Clinical and Neuroimaging Features

New-onset refractory status epilepticus (NORSE) is a rare but challenging condition occurring in a previously healthy patient, often with no identifiable cause. We describe the electro-clinical features and outcomes in a group of patients with NORSE who all demonstrated a typical magnetic resonance imaging (MRI) sign characterized by bilateral lesions of the claustrum. The group includes 31 patients (12 personal and 19 previously published cases; 17 females; mean age of 25 years). Fever preceded status epilepticus (SE) in 28 patients, by a mean of 6 days. SE was refractory/super-refractory in 74% of the patients, requiring third-line agents and a median of 15 days staying in an intensive care unit. Focal motor and tonic–clonic seizures were observed in 90%, complex partial seizures in 14%, and myoclonic seizures in 14% of the cases. All patients showed T2/FLAIR hyperintense foci in bilateral claustrum, appearing on average 10 days after SE onset. Other limbic (hippocampus, insular) alterations were present in 53% of patients. Within the personal cases, extensive search for known autoantibodies was inconclusive, though 7 of 11 patients had cerebrospinal fluid lymphocytic pleocytosis and 3 cases had oligoclonal bands. Two subjects died during the acute phase, one in the chronic phase (probable sudden unexplained death in epilepsy), and one developed a persistent vegetative state. Among survivors, 80% developed drug-resistant epilepsy. Febrile illness-related SE associated with bilateral claustrum hyperintensity on MRI represents a condition with defined clinical features and a presumed but unidentified autoimmune etiology. A better characterization of de novo SE is mandatory for the search of specific etiologies.
A data de-duplication access framework for solid state drives

With the rapid development of SSDs (Solid State Drives), traditional hard drives in many applications have been replaced by SSDs. Since SSDs consist of NAND flash memory, the main challenge to SSDs is that NAND flash memory is highly sensitive to write requests. A lot of write requests will cause garbage collection to reclaim free space due to the "out-place update" characteristic of flash memory. In the paper, we will propose a data de-duplication access framework for SSDs. The objective is to eliminate duplicate data as much as possible and reduce space consumption. According to the experimental results, the proposed framework can efficiently identify duplicate data and decrease a lot of data written, and at the same time, the overhead is also reasonable.
Secure Session Key Sharing Using Public Key Cryptography

In distributed systems, entities perform the predefined tasks distributively and have to communicate quite frequently. Confidentiality is the primary security requirement in such systems. There should be some secure mechanism whereby a pair of entities can securely communicate with each other. In most of the applications of distributed systems, computational and communication resources are limited and any such mechanism that ensures security of data under transmission should consider these computational and communicational constraints. Symmetric key cryptography emerges as one of the effective mechanisms to secure the data in distributed systems. The security of a symmetric key mechanism purely depends on the secrecy of the session key. In this paper, we have proposed a protocol for the sharing of session key between communicating entities securely. The proposed protocol secures the session through asymmetric key mechanism and once the session key is securely shared, the entities can communicate through the shared session key.
UvA-DARE ( Digital Academic Repository ) Plant structural changes due to herbivory : Do changes in Aceria-infested coconut fruits allow predatory mites to move under the perianth ?

Being minute in size, eriophyoid mites can reach places that are small enough to be inaccessible to their predators. The coconut mite, Aceria guerreronis, is a typical example; it Wnds partial refuge under the perianth of the coconut fruit. However, some predators can move under the perianth of the coconut fruits and attack the coconut mite. In Sri Lanka, the phytoseiid mite Neoseiulus baraki, is the most common predatory mite found in association with the coconut mite. The cross-diameter of this predatory mite is c. 3 times larger than that of the coconut mite. Nevertheless, taking this predator’s Xat body and elongated idiosoma into account, it is—relative to many other phytoseiid mites—better able to reach the narrow space under the perianth of infested coconut fruits. On uninfested coconut fruits, however, they are hardly ever observed under the perianth. Prompted by earlier work on the accessibility of tulip bulbs to another eriophyoid mite and its predators, we hypothesized that the structure of the coconut fruit perianth is changed in response to damage by eriophyoid mites and as a result predatory mites are better able to enter under the perianth of infested coconut fruits. This was tested in an experiment where we measured the gap between the rim of the perianth and the coconut fruit surface in three cultivars (‘Sri Lanka Tall’, ‘Sri Lanka Dwarf Green’ and ‘Sri Lanka Dwarf Green £ Sri Lanka Tall’ hybrid) that are cultivated extensively in Sri Lanka. It was found that the perianth-fruit gap in uninfested coconut fruits was signiWcantly diVerent between cultivars: the cultivar ‘Sri Lanka Dwarf Green’ with its smaller and more elongated coconut fruits had a larger perianth-fruit gap. In the uninfested coconut fruits this gap was large enough for the coconut mite to creep under the perianth, yet too small for its predator N. baraki. However, when the coconut fruits were infested by coconut mites, the perianth-rim-fruit gap was not diVerent among cultivars and had increased to such an extent that the space under the perianth became accessible to the predatory mites. N. S. Aratchige · M. W. Sabelis (&) · I. Lesna Section Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Kruislaan 320, Amsterdam, 1098 SM, The Netherlands e-mail: sabelis@science.uva. nl N. S. Aratchige Crop Protection Division, Coconut Research Institute, Lunuwila, 61150, Sri Lanka