Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic code symmetry and efficient design of GC-constrained coding sequences

MOTIVATION Cloning of long DNA sequences (40-60 bases) into phage display libraries using polymerase chain reaction (PCR) is a low efficiency process, in which PCR is used to incorporate a DNA insert, coding for a certain peptide, into the amplified sequence. The PCR efficiency in this process is strongly affected by the distribution of G-C bases in the amplified sequence. As any DNA insert coding for the target peptide may be attempted, there is a flexibility in choosing part of the amplified sequence. Since the number of inserts coding for the same peptide is exponential in the peptide length, a computational problem naturally arises--that of efficiently finding an insert, whose parameters are optimal for PCR cloning. RESULTS The GC distribution requirements are formulated as a search problem. We developed an efficient, linear time 'one pass' algorithm for this problem. Interestingly, our algorithm strongly relies on an interesting symmetry, which we observed in the standard genetic code. Most non-standard genetic codes examined possess this symmetry as well, yet some do not. We generalize the search problem and consider the case of a non-standard, or arbitrary, genetic code where this symmetry does not necessary hold. We solve the generalized problem in polynomial, but nonlinear, time. AVAILABILITY An implementation of the proposed algorithm is available upon request from the authors.
Mitochondria, the killer organelles and their weapons

Apoptosis is a cell‐autonomous mode of death that is activated to eradicate superfluous, damaged, mutated, or aged cells. In addition to their role as the cell's powerhouse, mitochondria play a central role in the control of apoptosis. Thus, numerous pro‐apoptotic molecules act on mitochondria and provoke the permeabilization of mitochondrial membranes. Soluble proteins contained in the mitochondrial intermembrane space are released through the outer membrane and participate in the organized destruction of the cell. Several among these lethal proteins can activate caspases, a class of cysteine proteases specifically activated in apoptosis, whereas others act in a caspase‐independent fashion, by acting as nucleases (e.g., endonuclease G), nuclease activators (e.g., apoptosis‐inducing factor), or serine proteases (e.g., Omi/HtrA2). In addition, mitochondria can generate reactive oxygen species, following uncoupling and/or inhibition of the respiratory chain. The diversity of mitochondrial factors participating in apoptosis emphasizes the central role of these organelles in apoptosis control and unravels novel mechanisms of cell death execution. © 2002 Wiley‐Liss, Inc.
The pharmacological management of cancer pain. Part 1: The role of non opioid and adjuvant drugs.

The incidence of pain among 5,410 patients at various stages of the disease was 51%, whereas among 9,007 patients with advanced metastatic or at terminal phase of cancer was 74% [1]. Furthermore, published data show that among advanced cancer patients with pain, the symptom is moderate to severe in about 40%-50% and very severe or excruciating in 25%30% [2-4] and that most advanced-cancer patients have two or more types and/or etiologies of cancerrelated pain [3-8]. One-third of adults and children with metastatic cancer report pain that interferes with and reduces their activity level and requires the use of analgesics [9]. The frequency of chronic cancer pain is related to the initial cancer site and varies from 85% (bone) to 5% (leukemia) [4]. Foley [4] found that among 143 cancer in patients referred for pain therapy, the pain was due to cancer in 78% and to cancer therapy in 19%. The nociceptive stimulus may be somatic (e.g., metastatic to bone, pleura involvement), visceral (e.g., distended bowel proximal to obstruction) or neuropathic as a result of aberrant processes in the peripheral or central nervous system that result from injury to neural pathways. Some of these neuropathic pains are due to deafferentation and may result from rumor infiltration of nerves (e.g., brachial plexopathy due to Pancoast's tumor) or surgical intervention (e.g., phantom limb pain). Table 1 summarizes various cancer-related pain syndromes. Assessment of cancer pain is essential in evaluating the current status of the patient, the pain and its impact on the patient as well as the efficacy of pain therapy over time. Different types of pain evaluation are available, as per the review by Chapman and Syrjala [10] and other papers [11-13]. Table 1. Pain syndromes in cancer patients.
Cataloguing of learning objects using social tagging

Social tagging has been recognized as an important solution to the description of resources available on the Web. In the context of e-learning it is presented as an auxiliary mechanism to the composition of learning object metadata. This article aims to present the results of a study on the state of the art of works related to social tagging and learning objects, promoting a discussion about the main elements related to the concepts.
Three-Dimensional Face Recognition Using Surface Space Combinations

In this paper we test a range of three-dimensional face recognition systems, based on the fishersurface method developed in previous work. We show the effect of using a variety of facial surface representations and suggest a method of identifying and extracting useful qualities offered by each system. Combing these components into a unified surface subspace, we create a threedimensional face recognition system producing significantly lower error rates than individual systems tested on the same data. We evaluate systems by performing up to 1,079,715 verification operations on a large test set of 3D face models. Results are presented in the form of false acceptance and false rejection rates, generated by varying a decision threshold applied to a distance metric in combined surface space.
D0-branes on $T^n$ and matrix theory

The Hamiltonian describing Matrix theory on T^n is identified with the Hamiltonian describing the dynamics of D0-branes on T^n in an appropriate weak coupling limit for all n up to 5. New subtleties arise in taking this weak coupling limit for n=6, since the transverse size of the D0 brane system blows up in this limit. This can be attributed to the appearance of extra light states in the theory from wrapped D6 branes. This subtlety is related to the difficulty in finding a Matrix formulation of M-theory on T^6.
State of the art: massive transfusion

The aim of this article was to review recent developments in the resuscitation of both trauma and non‐trauma patients in haemorrhagic shock. Strategies for the resuscitation of massively haemorrhaging patients and the use of massive transfusion protocols (MTPs) have been a major focus of the trauma literature over the past several years. The application of haemostatic resuscitation practices and MTPs to non‐trauma populations has long been in practice, but has only recently been the subject of active research. Medline and PubMed were reviewed for ‘massive transfusion’ (MT) from 2012 to present. Non‐English and paediatric articles were excluded. Articles were systematically reviewed for their relevance to MT. There were eight major areas of development identified. In recent MT literature, there was an increased focus on massively haemorrhaging non‐trauma patients, the role of acute traumatic coagulopathy, the use of thromboelastography (TEG), and the impact of MTPs on blood product waste and efficiency of product delivery. Other developments included additional MT prediction tools and The PRospective Observational Multicenter Major Trauma Transfusion (PROMMTT) study. There was also interest in re‐evaluating the clinical relevance of the current MT definition and identifying new foci for MT. These recent developments reflect efforts to better understand and manage non‐traumatic haemorrhage and to address prior limitations in the trauma literature. Inevitably, new questions have been raised, which will likely direct ongoing and future research in MT.
Efficient lock-free binary search trees

In this paper we present a novel algorithm for concurrent lock-free internal binary search trees (BST) and implement a Set abstract data type (ADT) based on that. We show that in the presented lock-free BST algorithm the amortized step complexity of each set operation - Add, Remove and Contains - is O(H(n) + c), where H(n) is the height of the BST with n number of nodes and c is the contention during the execution. Our algorithm adapts to contention measures according to read-write load. If the situation is read-heavy, the operations avoid helping the concurrent Remove operations during traversal, and adapt to interval contention. However, for the write-heavy situations we let an operation help a concurrent Remove, even though it is not obstructed. In that case, an operation adapts to point contention. It uses single-word compare-and-swap (CAS) operations. We show that our algorithm has improved disjoint-access-parallelism compared to similar existing algorithms. We prove that the presented algorithm is linearizable. To the best of our knowledge, this is the first algorithm for any concurrent tree data-structure in which the modify operations are performed with an additive term of contention measure.
Cooperative Traffic Light Control Based on Semi-real-time Processing

—In this paper, we investigate cooperative traffic light control for multiple intersections based on semi-real-time processing. As urban traffic congestion problems is increasingly aggravating, existing traffic light controllers can no longer satisfy the rising demands for efficiently easing traffic pressure. In this paper, we propose an adaptive traffic light control algorithm based on semi-real-time processing and cooperation among traffic light controllers. We set fixed phase duration between traffic light phases in advance. For each intersection, the controller determines the next traffic light phase by prediction of traffic situation for the next period. To evaluate our proposed algorithm, we construct four traffic scenarios and run simulations with combination of NS3 and SUMO. The simulation results demonstrate that our proposed algorithm is effective and practical in different scenarios; it can reduce traffic load and average waiting time of vehicles, as well as enhance traffic throughput of intersections.
Les OMD et l'aide de cinquième génération

Le renouvellement permanent des objectifs, des idees dominantes et des instruments d’aide est une realite qui s’impose a la communaute du developpement. Ce mouvement incessant est souvent associe a un phenomene de mode et plus rarement relie a un processus d’accumulation des connaissances. L’objet du present article est d’analyser l’evolution de la pensee sur le developpement a partir des differents fondements ethiques qui sous-tendent l’aide internationale.Pour cela l’article etudie un certain nombre de questions ethiques sous-jacentes au positionnement de la communaute du developpement. Il tente de montrer que la succession des reponses apportees a ces dilemmes ethiques est une grille de lecture pertinente pour comprendre l’enchainement des differents paradigmes du developpement.L’article examine avec cette grille de lecture les positions recentes adoptees par la communaute du developpement autour de la priorite donnee a la realisation des Objectifs du millenaire pour le developpement.
Phonetic coding methods for Malay names retrieval

Searching for person names has been very popular among users of information systems and search engines. Thus, the effectiveness, accuracy and appropriateness of search results are strongly emphasized. Information retrieval (IR) methods provide high impact in influencing the searching results. Efforts in improving the IR methods have been made due to the fact that names are not unique and have varieties of spelling. This will caused errors during the process of getting accurate names. Searching based on phonetic is said to be a suitable method to solve the aforementioned problem because names have limited spelling standards. Phonetic method is used to recognize and retrieve words that have the same pronunciation. The main aim of this paper is to test the effectiveness of phonetic coding method on Malay name retrieval using Soundex and modified-Asoundex (Asoundex is an Arabic Soundex). The experimental approach used to perform this research consists of two stages; program development and testing Malay name data sets. The development of programs referred to the existing algorithms to generate name code. Code generated from program will be compared with data contained in the test data. The effectiveness of the result is determined by comparing the output with the result obtained from both phonetic approaches. Evaluation is based on the precision and recall measures. The contribution of the research is to provide comparative accuracy of Malay name retrieval using Soundex and modified-Asoundex coding method. Result show that an average of 38.38% improvement of the precision measure has been achieved.
Integrating Theories of Motivation

Progress toward understanding human behavior has been hindered by discipline-bound theories, dividing our efforts. Fortunately, these separate endeavors are converging and can be effectively integrated. Focusing on the fundamental features of picoeconomics, expectancy theory, cumulative prospect theory, and need theory, we construct a temporal motivational theory (TMT). TMT appears consistent with the major findings from many other investigations, including psychobiology and behaviorism. The potential implications of TMT are numerous, affecting our understanding on a wide range of topics, including group behavior, job design, stock market behavior, and goal setting.
Vinculin phosphorylation at residues Y100 and Y1065 is required for cellular force transmission

ABSTRACT The focal adhesion protein vinculin connects the actin cytoskeleton, through talin and integrins, with the extracellular matrix. Vinculin consists of a globular head and tail domain, which undergo conformational changes from a closed auto-inhibited conformation in the cytoplasm to an open conformation in focal adhesions. Src-mediated phosphorylation has been suggested to regulate this conformational switch. To explore the role of phosphorylation in vinculin activation, we used knock-out mouse embryonic fibroblasts re-expressing different vinculin mutants in traction microscopy, magnetic tweezer microrheology, FRAP and actin-binding assays. Compared to cells expressing wild-type or constitutively active vinculin, we found reduced tractions, cytoskeletal stiffness, adhesion strength, and increased vinculin dynamics in cells expressing constitutively inactive vinculin or vinculin where Src-mediated phosphorylation was blocked by replacing tyrosine at position 100 and/or 1065 with a non-phosphorylatable phenylalanine residue. Replacing tyrosine residues with phospho-mimicking glutamic acid residues restored cellular tractions, stiffness and adhesion strength, as well as vinculin dynamics, and facilitated vinculin–actin binding. These data demonstrate that Src-mediated phosphorylation is necessary for vinculin activation, and that phosphorylation controls cytoskeletal mechanics by regulating force transmission between the actin cytoskeleton and focal adhesion proteins. Summary: Src-mediated phosphorylation on Y100 and Y1065 is a prerequisite for vinculin activation, and controls cytoskeletal mechanics by regulating force transmission between the actin cytoskeleton and focal adhesion proteins.
Fully Committed: Suicide Bombers' Motivation and the Quest for Personal Significance

A motivational analysis of suicidal terrorism is outlined, anchored in the notion of significance quest. It is suggested that heterogeneous factors identified as personal causes of suicidal terrorism (e.g. trauma, humiliation, social exclusion), the various ideological reasons assumed to justify it (e.g. liberation from foreign occupation, defense of one's nation or religion), and the social pressures brought upon candidates for suicidal terrorism may be profitably subsumed within an integrative framework that explains diverse instances of suicidal terrorism as attempts at significance restoration, significance gain, and prevention of significance loss. Research and policy implications of the present analysis are considered.
Association between C-reactive protein and features of the metabolic syndrome: a population-based study.

OBJECTIVE To assess the association of circulating levels of C-reactive protein, a sensitive systemic marker of inflammation, with different components of the metabolic syndrome. RESEARCH DESIGN AND METHODS Total cholesterol (TC), HDL cholesterol, triglycerides, uric acid, BMI , and prevalence of diabetes and hypertension were assessed in 747 men and 956 women aged 18-89 years who were participating in the population-based National Health and Nutrition Survey, which was carried out in former West Germany in 1987-1988. RESULTS There was a statistically significant positive crude correlation between C-reactive protein and TC (R = 0.19), TG (R = 0.29), BMI (R = 0.32), glucose (R = 0.11), and uric acid (R = 0.14) (all P < 0.0001). A negative correlation was found between C-reactive protein and HDL cholesterol (R = 0.13, P < 0.0001). The age-adjusted geometric means of C-reactive protein concentrations in subjects grouped according to the presence of 0-1, 2-3, and > or =4 features of the metabolic syndrome were 1.11, 1.27, and 2.16 mg/l, respectively, with a statistically highly significant trend (P < 0.0001). CONCLUSIONS The data suggest that a variety of features of the metabolic syndrome are associated with a systemic inflammatory response.
Genetic stabilization by p53 involves growth regulatory and repair pathways

p53 performs a plethora of activities, which are directed towards the maintenance of the genomic integrity and constitute its universal role as a tumor suppressor. 1000 to 10000 latent p53 molecules are permanently available in order to monitor DNA exchange processes in mitotically growing cells. After the introduction of major DNA injuries the levels of posttranslationally modified p53 proteins rise, which in turn transcriptionally signal transient cell cycle arrest or apoptotic cell death, depending on the extent of damage. Taken together, p53 inhibits the manifestation of genomic instabilities at different control levels both during naturally occurring metabolic processes and in response to genotoxic treatments.
Embedding of Cortical Representations by the Superficial Patch System

Pyramidal cells in layers 2 and 3 of the neocortex of many species collectively form a clustered system of lateral axonal projections (the superficial patch system—Lund JS, Angelucci A, Bressloff PC. 2003. Anatomical substrates for functional columns in macaque monkey primary visual cortex. Cereb Cortex. 13:15–24. or daisy architecture—Douglas RJ, Martin KAC. 2004. Neuronal circuits of the neocortex. Annu Rev Neurosci. 27:419–451.), but the function performed by this general feature of the cortical architecture remains obscure. By comparing the spatial configuration of labeled patches with the configuration of responses to drifting grating stimuli, we found the spatial organizations both of the patch system and of the cortical response to be highly conserved between cat and monkey primary visual cortex. More importantly, the configuration of the superficial patch system is directly reflected in the arrangement of function across monkey primary visual cortex. Our results indicate a close relationship between the structure of the superficial patch system and cortical responses encoding a single value across the surface of visual cortex (self-consistent states). This relationship is consistent with the spontaneous emergence of orientation response–like activity patterns during ongoing cortical activity (Kenet T, Bibitchkov D, Tsodyks M, Grinvald A, Arieli A. 2003. Spontaneously emerging cortical representations of visual attributes. Nature. 425:954–956.). We conclude that the superficial patch system is the physical encoding of self-consistent cortical states, and that a set of concurrently labeled patches participate in a network of mutually consistent representations of cortical input.
A Formal Specification Model for Hardware/Software Codesign

Embedded controllers for reactive real-time applications are implemented as mixed software-hardware systems. in this paper we present a model for specification, partitioning, and implementation of such systems. The model, called Codesign Finite State Machines (CFSMs), is based on FSMs and is particularly suited to a specific class of systems with relatively low algorithmic complexity. Pre-existing formal specification languages can be used by the designer to specify the intended behavior of the system and mapped into our model. CFSMs use a non-zero unbounded reaction delay model and hence can be indifferently implemented either in hardware or in software. The implementation only restricts the range of variation of some previously undefined delays, thus preserving formal properties of the specification across implementation refinements. The communication primitive event broadcasting, is low-level enough to be implemented efficiently and yet general enough to allow higher-level mechanisms (such as channels) to be defined by the designer.
Energy cost of treadmill running in non-trained females differing in body fat.

BACKGROUND The energy demands of movement may be characterised by the energy cost C, which indicates how much energy is needed to carry a body mass of 1 kg over a distance of 1 m. It is generally accepted that the lower C represents a lesser amount of mechanical work executed with the same efficiency. The purpose of this study was to assess the influence of body fat on energy cost of running in healthy non-trained females. METHODS Energy cost of running (C) was determined on the treadmill in a group of healthy non-trained females (N=63, mean age=39.+/-10.2 years, body mass=64.6+/-5.5 kg, height= 166.2+/-5.7 cm, VO2max.kg(-1)=35.0+/-3.6 ml.kg(-1)min(-1)), differing significantly in the percentage of body fat (18.9-30.2%), assessed by the 10 skinfold measurements. RESULTS Mean value of C was 3.97+/-0.07 J.kg(-1)m(-1). The lowest values of C were found in subjects with the lowest %BF (C ranged from 3.81 to 4.06 J.kg(-1). m(-1)). There is a significant positive correlation between C and %BF [C (J.kg(-1). m(-1))= 0.0185*%BF (%) + 3.5090; r=0.7805; p<0.001; r2=0.6091], C and body mass (BM) [C (J.kg(-1). m(-1)) = 0.0083*BM (kg) + 3.4384; r=0.6176; p<0.001; r2 = 0.3814], and C and free fat mass (FFM) [C (J.kg(-1). m(-1))=0.0087*FFM (kg) + 3.5543; r=0.3521; p<0.05; r2=0.1240]. There is a negative correlation between C and VO2max.kg(-1) [C (J.kg(-1). m(-1))=-0.0181* VO2max.kg(-1) (ml.kg(-1). min(-1)) +4.6071; r=-0.8810; p<0.0001; r2=0.7761], and VO2max.kg(-1) and %BF [VO2max.kg(-1) (ml.kg(-1). min(-1)) =-0.8401* %BF(%) + 54.1021; r=-0.7142; p<0.0001; r2=0.5101]. CONCLUSIONS From the collected data for untrained females we may conclude: first, the higher the training state (VO2max.kg(-1)), the lower the energy cost of running. Second, the energy cost of running C increases with the increase in body mass, %BF and FFM. Third, the training state decreases (VO2max.kg(-1)) with the increase in %BF.