Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality specifications: self pleasure for clinical laboratories or added value for patient management?

Abstract Analytical quality specifications play a key role in assuring and continuously improving high-quality laboratory services. However, I believe, that there are two “missing links” in the effective management of quality specifications in the delivery of laboratory services. The first is the evidence that pre-analytical variation and related problems are not taken into great consideration by laboratory professionals. The second missing link is the communication of quality specifications to clinicians and other possible stakeholders. If quality specifications represent “the level of performance required to facilitate clinical decision-making”, they cannot be used only for internal quality management procedures but must be communicated to facilitate clinical reasoning, decision-making and patient management. A consensus should be achieved in the scientific community on these issues to assure better utilization of laboratory data and, ultimately, improved clinical outcomes. Clin Chem Lab Med 2007;45:462–6.
Cross recurrence quantification analysis of mild cognitive impairment EEG under working memory condition

This work investigates the effectiveness of the nonlinear method of cross recurrence quantification analysis (CRQA) for classifying EEG of subjects with mild cognitive impairment (MCI) based on their synchronization levels. The synchronization levels are quantified using the CRQA recurrence rate (RR) of EEG under memory activation state of picture recollection (PICREC) for both inter and intra lobar levels. In inter lobar level, MCI EEG shows higher RR values of CRQA with statistical significance on all regions when compared to the EEG of normal control group (NC). In intra lobar analysis also, RR values of MCI are significantly higher but only in the temporal and parietal regions. Receiver operating characteristics (ROC) is used for classification of EEG of these two groups. A fair classification is obtained between the EEG of MCI and NC by using ROC analysis under this memory activation task state.
An automatic lesion detection using dynamic image enhancement and constrained clustering

In this work, we present a fast and robust method for lesions detection, primarily, a non-linear image enhancement is performed on T1 weighted magnetic resonance (MR) images in order to facilitate an effective segmentation that enables the lesion detection. First a dynamic system that performs the intensity transformation through the Modified sigmoid function contrast stretching is established, then, the enhanced image is used to classify different brain structures including the lesion using constrained fuzzy clustering, and finally, the lesion contour is outlined through the level set evolution. Through experiments, validation of the algorithm was carried out using both clinical and synthetic brain lesion datasets and an 84%–93% overlap performance of the proposed algorithm was obtained with an emphasis on robustness with respect to different lesion types.
Communist attempts to elicit false confessions from Air Force prisoners of war.

Abstract : This journal article discusses the coercive methods used by Chinese Communists to extract false confessions from U.S. Air Force men who were captured during the Korean War. Specifically, the methods were meant to induce compliance -- to undermine the resistance of the prisoner. The article includes a chart showing an outline of these methods, classified into eight general types, some illustrations of the specific forms these methods take, and the author's judgment of the effect of each. The methods are as follows: isolation, monopolization of perception, induced debilitation or exhaustion, threats, occasional indulgences, demonstrating "omnipotence" and "omniscience," degradation, and enforcing trivial demands. The kind of "confession" discussed consists of considerably more than the signing of a piece of paper which says "On such and such a date I committed such and such a crime-signed John Jones. " It consists of considerably more than making an equivalent oral statement in a court. These "confession"-extortion efforts involve the attempt to manipulate the individual so that he behaves over an extended period as if: (1) he actually committed certain concrete acts which he can "describe" with meticulous detail; (2) these acts were "criminal," in the sense of being violations of the most fundamental standards of human decency; (3) these acts were not isolated transgressions but manifestations of a "criminal" pattern in his thought and action; (4) his "crimes" were part and parcel of a larger nefarious political conspiracy; (5) his "criminal" role was motivated by a self-seeking alignment with this political conspiracy, of which he was only a pawn; (6) he is now remorseful and repentant; and (7) his changed attitude is due to a new-found political conviction for which he is indebted to his patient captors.
Obliquebanded leafroller (Lepidoptera: Tortricidae) resistance to insecticides in Michigan apple and cherry orchards

“The escalating concern about resistance in C. rosaceana field populations has reinforced the need for continued resistance monitoring and identification of effective tools for integrated pest management programs. ” The native North American pest, obliquebanded leafroller, Choristoneura rosaceana (Harris) (Lepidoptera: Tortricidae), is widely distributed and has a broad range of over 50 hosts, but members of the Rosaceae family are preferred (Sanderson and Jackson 1909; Larocque et al. 1999). The p o l y p h a g o u s larva is the injurious stage of C. rosaceana, as it feeds on flower buds, leaves, and developing fruit (Sanderson and Jackson 1909; Reissig 1978). C. rosaceana is a foliage and fruit feeding pest in apple, causing significant damage, especially by the summer generation. In cherry, the foliage and fruit injury caused by C. rosaceana is less serious compared with apple. However, C. rosaceana is a more critical pest in cherry in the late season, when the larvae can be a contaminant in harvested cherries, thus representing a high risk for load rejection due to the U.S. Department of Agriculture zero-tolerance mandate (USDA 1941; Mason and Huber 2002; Wise and Whalon 2009). Historically, C. rosaceana was considered a secondary pest in fruit orchards, but it became a serious pest causing significant damage since outbreak populations began to occur in the late 1970s (Sial and Brunner 2010a, 2012b). Documentation of many cases of insecticide resistance in C. rosaceana populations against conventional insecticides has made this pest problem even more serious (Mushtaq et al. 2002; Smirle et al. 2002, 2003; Sial and Brunner 2012a). Conventional insecticides, especially the organophosphates, were the backbone of control programs at that time, and the resistance phenomenon among C. rosaceana populations against these compounds led to field failures in commercial apple control programs (Bostanian et al. 1985; Waldstein and Reissig 2000; Mushtaq et al. 2002; Sial and Brunner 2012b). Concurrent with the aggravating factor of resistance problems, US Congress passed the Food Quality Protection Act (FQPA) in 1996, which restricted or prevented the use of many conventional insecticides. As a consequence, fruit growers were forced to replace many of the conventional insecticides with This research was funded by Michigan Project GREEEN, Michigan Apple Committee and Michigan Cherry Committee
Simkania negevensis in community-acquired pneumonia in Italian children

Simkania negevensis, a recently found Chlamydia-like organism, has been associated with respiratory infections in children and adults with pneumonia, but S. negevensis findings have been common also without any infection. The aims of the present paper were to evaluate S. negevensis in the aetiology of paediatric community-acquired pneumonia (CAP), its seroprevalence in north Italian children, and whether there is cross-reactivity between S. negevensis and Chlamydia pneumoniae serology. Antibodies to S. negevensis were measured by microimmunofluorescence (MIF) in 101 frozen paired sera obtained from children with CAP. Serological evidence (>/=4-fold increase or decrease in IgM or IgG) of acute S. negevensis infection was achieved in 5 (5%) cases. Two were mixed infections with Mycoplasma pneumoniae and 1 with respiratory syncytial virus. In total, 20–30% of the children had measurable antibodies to S. negevensis, with no association with age. No cross-reactivity was observed between antibodies to S. negevensis and C. pneumoniae. S. negevensis appears to be a real, though rare, cause of CAP in children.
Generating automatic pseudo-entailments from AMR parses

We explore how to generate a textual inference dataset from Abstract Meaning Representations (AMR) (Banarescu et al., 2013). Various aspects of AMR make it problematic to automatically derive inference patterns. Therefore, our generated dataset instead answers questions regarding the relation between entities and actions in sentences. We refer to these answers as pseudo-entailments. From this dataset, it is possible to then extract entailments from sentences.
The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis

High‐molecular‐weight arginine‐ and lysine‐specific (Kgp) gingipains are essential virulence factors expressed by the oral pathogen Porphyromonas gingivalis. Haemagglutinin/adhesin (HA) regions of these proteases have been implicated in targeting catalytic domains to biological substrates and in other adhesive functions. We now report the crystal structure of the K3 adhesin domain/module of Kgp, which folds into the distinct β‐jelly roll sandwich topology previously observed for K2. A conserved structural feature of K3, previously observed in the Kgp K2 module, is the half‐way point anchoring of the surface exposed loops via an arginine residue found in otherwise highly variable sequences. Small‐angle X‐ray scattering data for the recombinant construct K1K2K3 confirmed a structure comprising a tandem repeat of three homologous modules, K1, K2 and K3 while also indicating an unusual ‘y’‐shape arrangement of the modules connected by variable linker sequences. Only the K2 and K3 modules and a K1K2 construct were observed to be potently haemolytic. K2, K3 and the K1K2 construct showed preferential recognition of haem‐albumin over albumin whereas only low affinity binding was detected for K1 and the K1K2K3 construct. The data indicate replication of some biological functions over the three adhesin domains of Kgp while other functions are restricted.
Isolation and characterization of polymorphic microsatellites for the bastard sole (Microchirus azevia)

The bastard sole (Microchirus azevia) is a species of commercial interest in Spain. Nevertheless, little information is currently available about the genetic characteristics of wild populations. In this survey, we have developed eight new microsatellites using an enriched genome library protocol. Primers were screened on a total of 54 individuals from two wild populations (Mediterranean and Atlantic) from the south coast of Spain, revealing six to 18 alleles per locus with expected heterozygosities ranging from 0.51 to 0.94. These markers can potentially be useful tools for use in population genetic studies.
Expression of estrogen receptor in diseased human prostate assessed by non‐radioactive in situ hybridization and immunohistochemistry

To understand the role of estrogen in the pathogenesis of benign prostatic hyperplasia, expressions of estrogen receptor (ER) mRNA and ER protein by in situ hybridization and by immunohistochemistry, respectively, were investigated in human prostatic tissues. In non‐malignant region, ER mRNA and ER protein were found in cytoplasm and nucleus, respectively, of stromal cells, but not in glandular epithelial and basal cells. In benign regions, ER mRNA/ER protein positive cells were found in fibromyoadenomatous and myoadenomatous hyperplasia, but not in adenomatous hyperplasia. A striking feature was periacinar arrangement of ER mRNA/ER protein positive stromal cells in all prostate carcinoma treated with androgen withdrawal. The ER mRNA/ER protein positive cells were immunohistochemically identified as fibroblasts, myoblasts, and smooth muscle cells. These results indicate that stromal cells are the primary target of estrogen in prostate, and that androgen withdrawal upregulates the expression of ER gene. © 1995 Wiley‐Liss, Inc.
Functional and Structural Brain Connectivity in Children With Bilateral Cerebral Palsy Compared to Age-Related Controls and in Response to Intensive Rapid-Reciprocal Leg Training

Background Compared to unilateral cerebral palsy (CP), less is known about brain reorganization and plasticity in bilateral CP especially in relation or response to motor training. The few trials that reported brain imaging results alongside functional outcomes include a handful of studies in unilateral CP, and one pilot trial of three children with bilateral CP. This study is the first locomotor training randomized controlled trial (RCT) in bilateral CP to our knowledge reporting brain imaging outcomes. Methods Objective was to compare MRI brain volumes, resting state connectivity and white matter integrity using DTI in children with bilateral CP with PVL and preterm birth history (<34 weeks), to age-related controls, and from an RCT of intensive 12 week rapid-reciprocal locomotor training using an elliptical or motor-assisted cycle. We hypothesized that connectivity in CP compared to controls would be greater across sensorimotor-related brain regions and that functional (resting state) and structural (fractional anisotropy) connectivity would improve post intervention. We further anticipated that baseline and post-intervention imaging and functional measures would correlate. Results Images were acquired with a 3T MRI scanner for 16/27 children with CP in the trial, and 18 controls. No conclusive evidence of training-induced neuroplastic effects were seen. However, analysis of shared variance revealed that greater increases in precentral gyrus connectivity with the thalamus and pons may be associated with larger improvements in the trained device speed. Exploratory analyses also revealed interesting potential relationships between brain integrity and multiple functional outcomes in CP, with functional connectivity between the motor cortex and midbrain showing the strongest potential relationship with mobility. Decreased posterior white matter, corpus callosum and thalamic volumes, and FA in the posterior thalamic radiation were the most prominent group differences with corticospinal tract differences notably not found. Conclusions Results reinforce the involvement of sensory-related brain areas in bilateral CP. Given the wide individual variability in imaging results and clinical responses to training, a greater focus on neural and other mechanisms related to better or worse outcomes is recommended to enhance rehabilitation results on a patient vs. group level.
AXR4 Is Required for Localization of the Auxin Influx Facilitator AUX1

The AUX1 and PIN auxin influx and efflux facilitators are key regulators of root growth and development. For root gravitropism to occur, AUX1 and PIN2 must transport auxin via the lateral root cap to elongating epidermal cells. Genetic studies suggest that AXR4 functions in the same pathway as AUX1. Here we show that AXR4 is a previously unidentified accessory protein of the endoplasmic reticulum (ER) that regulates localization of AUX1 but not of PIN proteins. Loss of AXR4 resulted in abnormal accumulation of AUX1 in the ER of epidermal cells, indicating that the axr4 agravitropic phenotype is caused by defective AUX1 trafficking in the root epidermis.
A framework for learning from demonstration, generalization and practice in human-robot domains

This dissertation presents a framework that enables robots to learn complex tasks from one or several demonstrations by a teacher, based on a set of available underlying robot capabilities. The framework, inspired from the approach people use when teaching each other through demonstration, uses an action-embedded approach for task representation, and uses learning by having the robot perform the task along with the teacher during the demonstration. Among humans, teaching skills or tasks is a complex process that relies on multiple means of interaction and learning, both on the part of the teacher and of the learner. In robotics, however, skill teaching has largely been addressed by using only one or very few of these modalities. This dissertation presents a novel approach that uses multiple modalities for instruction and learning, allowing a robot to learn representations of high-level, sequential tasks from instructive demonstrations, generalization over multiple but sparse demonstrations and by practicing under a teacher's supervision. To enable this type of learning, the underlying robot control architecture should exhibit the following key properties: modularity, reusability of existing modules, robustness and real-time response, support for learning and the ability to encode complex task representations. Behavior-based control (BBC) is an effective methodology for robot control, which provides modularity and robust real-time properties, but is limited with respect to the other capabilities listed above. This dissertation extends the standard BBC in that: (i) it allows for the representation and execution of complex, hierarchically structured tasks within a behavior-based framework; (ii) it enables reusability of behaviors through the use of generation of a behavior-based system. The experimental validation and evaluation presented in the dissertation demonstrate that the proposed task representation, in conjunction with multiple instructional modalities, provides an effective approach for robot learning of high-level sequential tasks, based on a set of underlying capabilities (behaviors).
An integrated information-based similarity measurement of gene ontology terms

Measuring the semantic similarity between pairs of terms in Gene Ontology (GO) can help to compare genes that can not be compared by other computational methods. In this study, we proposed an integrated information-based similarity measurement (IISM) to calculate the semantic similarity between two GO terms by taking into account multiple common ancestors that they share, and aggregating the semantic information and depth information of the non-redundant common ancestors. Our method searches for non-redundant common ancestors in an effective way. Validation experiments were conducted on both gene expression dataset and pathway dataset, and the experimental results suggest the superiority of our method against some existing methods.
Removal of Linear and Branched Alkylphenols from Aqueous Solutions with Horseradish Peroxidase

Alkylphenols were effectively treated with horseradish peroxidase at pH 7.0 and 30 °C in the presence of H2O2 and poly(ethylene glycol) irrespective of the relative position or isomeric form of the alkyl chains. Water-insoluble oligomer precipitates were readily filtered out after enzymatic treatment, and transparent and colorless solutions were obtained for all p- and m-alkylphenols used.
Peroxynitrite‐mediated oxidative damage to brain mitochondria: Protective effects of peroxynitrite scavengers

Peroxynitrite‐mediated oxidative damage has been implicated in brain mitochondrial respiratory dysfunction after traumatic brain injury (TBI), which precedes the onset of neuronal loss. The aim of this study was to investigate the detrimental effects of the peroxynitrite donor SIN‐1 (3‐morpholinosydnonimine) on isolated brain mitochondria and to screen penicillamine, a stoichiometric (1:1) peroxynitrite‐scavenging agent, and tempol, a catalytic scavenger of peroxynitrite‐derived radicals, as antioxidant mitochondrial protectants. Exposure of the isolated mitochondria to SIN‐1 caused a significant dose‐dependent decrease in the respiratory control ratio and was accompanied by a significant increase in state II respiration, followed by significant decreases (P < 0.05) in states III and V. These functional alterations occurred together with significant increases in mitochondrial protein carbonyl (PC), lipid peroxidation–related 4‐hydroxynonenal (4‐HNE), and 3‐nitrotyrosine (3‐NT) content. Penicillamine hydrochloride (10 μM) partially but significantly (P < 0.05) protected against SIN‐1‐induced decreases in states III and V. However, a 2.5 μM concentration of tempol was able to significantly antagonize a 4‐fold molar excess (10 μM) concentration of SIN‐1 as effectively as were higher tempol concentrations, consistent with the likelihood that tempol works by a catalytic mechanism. The protection of mitochondrial respiration by penicillamine and tempol occurred in parallel with attenuation of PC, 4‐HNE, and 3‐NT. These results indicate that SIN‐1 causes mitochondrial oxidative damage and complex I dysfunction and that antioxidant compounds that target either peroxynitrite or its radicals may be effective mitochondrial protectants in the treatment of neural injury. © 2007 Wiley‐Liss, Inc.
Origin of Substrate Specificity of Human and Rat 17β-Hydroxysteroid Dehydrogenase Type 1, Using Chimeric Enzymes and Site-Directed Substitutions.

Human 17beta-hydroxysteroid dehydrogenase (17-HSD) type 1 predominantly catalyzes the 17beta-reduction of estrone to estradiol. The present results, however, show that rat 17-HSD type 1 equally uses both estrone and androstenedione as substrates. Analyzing the activity of various rat/human chimeric enzymes indicated that the region between amino acids 148 and 268 is responsible for the difference in substrate specificity, which is in line with the structural data showing that the recognition end of the active site is primarily at residues 185-230. The enzymes are highly conserved between amino acids 148-191, and the data indicate that in this region Asn152HisAsp153Glu and Pro187Ala variations are most closely related to the differential steroid specificity. The structural analyses furthermore suggested that the presence of His instead of Asn at position 152 of the human enzyme might result in considerable rearrangement of the loop located close to the beta-face of the A- and B-rings of the bound substrate, and that the Pro187Ala variation could modify the flexible region involved in substrate recognition and access of the substrate to the active site. Altogether, our results indicate that the Asn152His and Pro187Ala variations, together with several amino acid variations at the recognition end of the catalytic cleft built by residues 190-230, alter the structure of the active site of rat 17-HSD type 1 to one more favorable to an androgenic substrate.