Miracle-dz/UniFAR-FTUs huggingface dataset:
The stiffness of lymph nodes containing lung carcinoma metastases

It is believed that the stiffness or hardness of a lymph node containing a metastasis differs from that of lymph node without a metastasis because of the difference in tissue density, which is derived from the lymph node's histopathologic features. Prior to this study, however, there had been no attempts to quantify the hardness or stiffness of lymph nodes. The authors developed a new tactile sensor and system for measuring the stiffness (g/cm) of lymph nodes accurately, and they studied its utility as a tool for diagnosing lymph node metastases.
Changes in skeletal muscle size, fibre‐type composition and capillary supply after chronic venous occlusion in rats

Aim: We have previously shown that surgical occlusion of some veins from skeletal muscle results in muscle hypertrophy without mechanical overloading in the rat. The present study investigated the changes in muscle‐fibre composition and capillary supply in hypertrophied muscles after venous occlusion in the rat hindlimb.
Gambling Attitudes and Financial Misreporting

We investigate whether attitudes toward gambling help explain the occurrence of intentional misreporting. Similar to gambling, some financial reporting choices involve taking deliberate, speculative risks. We predict that in places where gambling is more socially acceptable, managers will be more likely to take financial reporting risks that increase the likelihood the financial statements will need to be restated. To test this prediction, we exploit geographic variation in local gambling attitudes and find that restatements due to intentional misreporting are more common in areas where gambling is more socially acceptable. This association is even stronger in situations where management is under greater pressure to misreport, including when the firm is close to meeting a performance benchmark, experiencing poor financial performance, or under investment‐related pressure. Furthermore, these results are robust to numerous tests to address omitted variables and endogeneity. Collectively, these findings suggest gambling attitudes help explain the incidence of intentional misreporting. Les auteurs se demandent si les attitudes a l’egard du jeu contribuent a expliquer l'occurrence de la falsification intentionnelle de l'information financiere. En matiere d'information financiere, certains choix apparentes au jeu font intervenir la prise intentionnelle de risques speculatifs. Selon la prediction des auteurs, la ou le jeu est davantage acceptable socialement, les gestionnaires seront plus susceptibles de prendre, au chapitre de l'information financiere, des risques augmentant la probabilite qu'un retraitement des etats financiers s'impose. Pour verifier cette prediction, les auteurs exploitent la fluctuation des attitudes a l’egard du jeu selon la situation geographique et constatent que les retraitements exiges par la falsification intentionnelle de l'information financiere sont plus courants la ou le jeu est davantage acceptable socialement. Cette association est meme plus marquee encore lorsque les gestionnaires sont plus fortement incites a falsifier l'information financiere, notamment si la societe est sur le point d'atteindre un indicateur de performance ou d'enregistrer une pietre performance, ou qu'elle est soumise a des pressions liees a l'investissement. En outre, ces resultats resistent a de nombreux tests visant a prendre en compte les variables omises et a traiter l'endogeneite. Dans l'ensemble, ces observations semblent indiquer que les attitudes a l’egard du jeu contribuent a expliquer l'incidence de la falsification intentionnelle de l'information financiere.
Importance of eye position on spatial localization in blind subjects wearing an Argus II retinal prosthesis.

PURPOSE With a retinal prosthesis connected to a head-mounted camera (camera-connected prosthesis [CC-P]), subjects explore the visual environment through head-scanning movements. As eye and camera misalignment might alter the spatial localization of images generated by the device, we investigated if such misalignment occurs in blind subjects wearing a CC-P and whether it impacts spatial localization, even years after the implantation. METHODS We studied three subjects blinded by retinitis pigmentosa, fitted with a CC-P (Argus II) 4 years earlier. Eye/head movements were video recorded as subjects tried to localize a visual target. Pointing coordinates were collected as subjects were requested to orient their gaze toward predetermined directions, and to point their finger to the corresponding perceived spot locations on a touch screen. Finally, subjects were asked to give a history of their everyday behavior while performing visually controlled grasping tasks. RESULTS Misaligned head and gaze directions occurred in all subjects during free visual search. Pointing coordinates were collected in two subjects and showed that median pointing directions shifted toward gaze direction. Reportedly all subjects were unable to accurately determine their eye position, and they developed adapted strategies to perform visually directed movements. CONCLUSIONS Eye position affected perceptual localization of images generated by the Argus II prosthesis, and consequently visuomotor coordination, even 4 years following implantation. Affected individuals developed strategies for visually guided movements to attenuate the impact of eye and head misalignment. Our observations provide indications for rehabilitation procedures and for the design of upcoming retinal prostheses. (ClinicalTrials.gov number, NCT00407602.).
Slim-tree and BitMatrix index structures in image retrieval system using MPEG-7 Descriptors

Content-based retrieval of multimedia data has still been an active research area. The efficient retrieval in natural images has been proven a difficult task for content-based image retrieval systems. In this paper, we present a system that adapts two different index structures, namely Slim-Tree and BitMatrix, for efficient retrieval of images based on multidimensional low-level features such as color, texture and shape. These index structures also use metric space. We use MPEG-7 Descriptors extracted from images to represent these features and store them in a native XML database. The low-level features; color layout (CL), dominant color (DC), edge histogram (EH) and region shape (RS) are used in Slim-Tree and BitMatrix and aggregated by ordered weighted averaging (OWA) method to find final similarity between any two objects. The experiments included in the paper are in the subject of index construction and update, query response time and retrieval effectiveness using ANMRR performance metric and precision/recall scores. The experimental results strengthen the case that uses BitMatrix along with ordered weighted averaging method in content-based image retrieval systems.
Lack of effect of compartmentalized drug resistance mutations on HIV-1 pol divergence in antiretroviral-experienced women

Objective:To examine the persistence of compartmentalized HIV drug resistance mutations (DRM) over time in the female genital tract and its effect on pol gene divergence compared to that in blood. Design:Longitudinal cohort of 22 antiretroviral-experienced women in the Emory Vaginal Ecology study. Methods:Blood and vaginal secretions were collected at serial clinic visits. DRM in the HIV reverse transcriptase and protease regions of pol were determined using population based sequencing. Kimura-2 pairwise DNA distances were calculated to measure blood and vaginal secretions divergence in the intervals between clinic visits. Results:Only eight (36%) women had compartmentalized DRM detected at 14 (31%) of their 45 clinic visits. This compartmentalized resistance was transient; 13 of 14 mutations in blood and all 12 mutations in vaginal secretions were compartmentalized for only one clinic visit. Over time, divergence of both reverse transcriptase and protease were greater in vaginal secretions than in blood. However, divergence in blood, but not in vaginal secretions, increased significantly in the presence of drug resistance or compartmentalized drug resistance. Conclusion:Compartmentalized DRM between the blood and vaginal secretions are transient in nature, and the presence of DRM does not affect pol gene divergence in the vaginal secretions. Our results provide new evidence that the genital mucosa does not support an independently evolving subpopulation of HIV-1 genomes.
Serum cystatin C in mouse models: a reliable and precise marker for renal function and superior to serum creatinine.

BACKGROUND Serum creatinine (SCR) and blood urea nitrogen (BUN) determine the glomerular filtration rate (GFR) improperly in acute renal failure. Serum cystatin C (CYS) has the potential to be a more precise marker for GFR. The aim of this study was to compare the sensitivity of SCR, BUN and CYS with respect to the detection of acute renal failure in mice. METHODS In an ischaemia reperfusion (I/R) injury model, mice suffered 60-min left kidney ischaemia and right nephrectomy. In a nephrectomy model, mice were nephrectomized to a different extent: from unilateral (3/6Nx) to bilateral nephrectomy (BiNx). Blood samples were collected 2, 12 or 24 h post-op. RESULTS SCR, BUN and CYS increased significantly in the I/R-model in comparison to sham mice and 3/6Nx mice at 12 and 24 h post-op (SCR P = 0.009; BUN P < 0.001 and CYS P < 0.004). There were no significant differences in all three markers between 3/6Nx and sham-operated mice. In graded nephrectomy, BUN and CYS showed already significantly the loss of kidney in 4/6Nx mice 12 h post-op [BUN (mg/dl): sham 26.4 +/- 3.5, 4/6Nx 52.3 +/- 13.4, P < 0.01; CYS (mg/l): sham 0.08 +/- 0.03, 4/6Nx 0.15 +/- 0.04, P < 0.01], whereas SCR was only significantly increased in 5/6Nx and BiNx mice 24 h post-op [SCR (mg/dl): sham 0.39 +/- 0.05, 4/6Nx 0.52 +/- 0.07, P = 0.13, 5/6Nx 1.00 +/- 0.29, P < 0.01]. In the longitudinal experiment, CYS showed the renal damage significantly earlier and to a larger extent (2 h: SCR 57 +/- 15%, BUN 40 +/- 16%, CYS 295 +/- 143%, P <0.001). CONCLUSIONS CYS can be used as a reliable and precise marker for renal function in mouse models. CYS is more sensitive than SCR, and it shows renal damage earlier than SCR and BUN.
New Vectorcardiographic non-planarity measure of T-wave loop improves separation between healthy subjects and myocardial infarction patients

Principal component analysis of vectorcardio-graphic T-wave loop has been shown to be a potential tool to describe the abnormality of the cardiac repolarization and to predict cardiac events in patients with cardiac disease. In this paper a new method for estimating the non-planarity of the T-wave loop is introduced and tested with healthy subjects and subjects with anterior or inferior myocardial infarction. The method is based on the resamping of T-wave data points with respect to the arc-length, the total least squares plane fitting, the identifying and reordering of the fitted axes, and decomposing the optimal rotation matrix. A recently published related measure, PCA3, was used for comparison purposes. The results showed that the non-planarity of T-wave loop increased significantly in patients with myocardial infarction compared to the healthy group. The new method separated healthy and patient groups with p-value 0.002 while PCA3 only with p-value 0.075. The new method was superior to PCA3 in separating the healthy patients from both infarction types.
Repeated Sprint Training Improves Intermittent Peak Running Speed in Team-Sport Athletes

Hunter, JR, O'Brien, BJ, Mooney, MG, Berry, J, Young, WB, and Down, N. Repeated sprint training improves intermittent peak running speed in team-sport athletes. J Strength Cond Res 25(5): 1318-1325, 2011-The aim of this study was to compare the effect of 2 repeated sprint training interventions on an intermittent peak running speed (IPRS) test designed for Australian Rules football. The test required participants to perform 10 × 10-m maximal efforts on an 80-m course every 25 seconds, for each of which the mean peak speed (kilometers per hour) was recorded to determine IPRS. The training interventions were performed twice weekly for 4 weeks immediately before regular football training. In the constant volume intervention (CVol), sprint repetition number remained at 10 (n = 9), and in the linear increase in volume (LIVol) intervention, repetition number increased linearly each week by 2 repetitions (n = 12). Intermittent peak running speed, 300-m shuttle test performance, and peak running speed were assessed before and upon completion of training. All measures were compared to a control group (CON; n = 8) in which players completed regular football training exclusively. Intermittent peak running speed performance in CVol and LIVol improved significantly (p < 0.01) by 5.2 and 3.8%, respectively, with no change in IPRS for CON. There were no differences in IPRS changes between CVol and LIVol. Additionally, peak running speed improved significantly (p < 0.01) by 5.1% for CVol, whereas 300-m shuttle performance improved significantly (p < 0.01) by 2.6% for LIVol only. Intermittent peak running speed, 300-m shuttle performance and peak running speed were improved after 4 weeks of training; however, progressively increasing sprint repetition number had no greater advantage on IPRS adaptation. Additionally, exclusive regular football training over a 4-week period is unlikely to improve IPRS, peak running speed, or 300-m shuttle performance.
Does Disparate Occurrence of Autoregulatory Programmed Frameshifting in Decoding the Release Factor 2 Gene Reflect an Ancient Origin with Loss in Independent Lineages?

ABSTRACT In Escherichia coli an autoregulatory mechanism of programmed ribosomal frameshifting governs the level of polypeptide chain release factor 2. From an analysis of 20 sequences of genes encoding release factor 2, we infer that this frameshift mechanism was present in a common ancestor of a large group of bacteria and has subsequently been lost in three independent lineages.
Response of pancreatic cancer cells treated with interferon-α or β and co-exposed to ionising radiation

Purpose: Clinical trials on pancreatic cancer demonstrated that interferons (IFN) improve the therapeutic index of combined radio- and chemotherapy. This is believed to be due to radiosensitisation of cells, which, however, needs experimental verification. Materials and methods: Here, we compared the survival response of ten pancreatic tumour cell lines following ionising radiation (IR), interferon-α (IFN-α), interferon-β (IFN-β) and combined treatment. The effect of combination treatment on apoptosis induction was also determined. Results: In most cell lines IFN treatment on its own exerted cytotoxicity, which was independent of the expression level of the IFN receptor on the cell surface. Three cell lines showed a radiosensitisation effect while two showed radioprotection. Although IFN-α is commonly used in the clinic, IFN-β induced a stronger cytotoxic response than IFN-α in vitro. The likely mechanism of enhancement of radiosensitivity in the responsive cell lines was shown to be an increase of the radiation-induced apoptotic response by IFN pretreatment. Conclusions: Given that the in vitro data do not conform to the impressive clinical results observed after combined radio- and chemotherapy with IFN-α, it is reasonable to conclude that the sensitising effect of IFN is not mediated through modulating the intrinsic radiosensitivity of pancreatic cancer cells.
Using encapsulated MEMS resonators to measure evolution in thin film stress

Encapsulated resonators can offer excellent long-term frequency stability, because the encapsulation provides protection from external environmental variations. Encapsulated double-anchored flexural-mode resonators exhibit a sensitive coupling between changes in stresses applied to the chip and changes in the resonant frequency while still isolated from other external variations. In this work, this sensitivity is exploited to observe stress relaxation in thin films deposited on the outside of the encapsulated resonator. Because of the high sensitivity to stress, and the insensitivity to other factors, these devices provide the first opportunity to observe film stress relaxation with nano-strain resolution. We have begun a study of film stress relaxation in LPCVD and TEOS oxides and aluminum-all of which are commonly used as structural layers in MEMS devices. Theoretical analysis, finite element analysis (FEA), as well as preliminary data on different film materials are presented herein.
Automatic Bias of Temporal Expectations following Temporally Regular Input Independently of High-level Temporal Expectation

Exposure to rhythmic stimulation results in facilitated responses to events that appear in-phase with the rhythm and modulation of anticipatory and target-evoked brain activity, presumably reflecting “exogenous,” unintentional temporal expectations. However, the extent to which this effect is independent from intentional processes is not clear. In two EEG experiments, we isolated the unintentional component of this effect from high-level, intentional factors. Visual targets were presented either in-phase or out-of-phase with regularly flickering colored stimuli. In different blocks, the rhythm could be predictive (i.e., high probability for in-phase target) or not, and the color could be predictive (i.e., validly cue the interval to the target) or not. Exposure to nonpredictive rhythms resulted in faster responses for in-phase targets, even when the color predicted specific out-of-phase target times. Also, the contingent negative variation, an EEG component reflecting temporal anticipation, followed the interval of the nonpredictive rhythm and not that of the predictive color. Thus, rhythmic stimulation unintentionally induced expectations, even when this was detrimental. Intentional usage of predictive rhythms to form expectations resulted in a stronger behavioral effect, and only predictive cues modulated the latency of the target-evoked P3, presumably reflecting stimulus evaluation. These findings establish the existence of unintentional temporal expectations in rhythmic contexts, dissociate them from intentional expectations, and highlight the need to distinguish between the source of expectation (exogenous–endogenous) and the level of voluntary control involved in it (unintentional–intentional).
A novel information contents based similarity metric for comparing TFBS motifs

Identifying binding sites recognized by transcription factors (TFs) is one of major challenges to decipher complex genetic regulatory networks encoded in a genome. A set of binding sites recognized by the same TF, called a motif, can be accurately represented by a position frequency matrix (PFM) or a position-specific scoring matrix (PSSM). Very often, we need to compare motifs when searching for similar motifs in a motif database for a query motif, or clustering motifs possibly recognized by the same TF. In this paper, we have designed a novel metric, called SPIC (Similarity between Positions with Information Contents), for quantifying the similarity between two motifs using their PFMs, PSSMs, and column information contents, and demonstrated that this metric outperforms the other state-of-the-art methods for clustering motifs of the same TF and differentiating motifs of different TFs.
EXPRESSION PROFILING OF THE MANNURONAN C5‐EPIMERASE MULTIGENIC FAMILY IN THE BROWN ALGA LAMINARIA DIGITATA (PHAEOPHYCEAE) UNDER BIOTIC STRESS CONDITIONS 1

The aim of this study was to profile expression of mannuronan C5‐epimerase (ManC5‐E) genes of Laminaria digitata (Huds.) J. V. Lamour. under treatment with brown alga cell wall components known to induce defense reaction in this organism. After determining that incubation in the presence of homo‐guluronates increased the accumulation of ManC5‐E transcripts, we cloned a number of partial ManC5‐E genes from nonelicited and elicited specimens. In addition to these fragments, previously identified genes from sporophyte and protoplast cDNA libraries were considered for a clustering analysis. Several groups of ManC5‐E genes were observed, including groups containing sequences specific from nonelicited and elicited sporophytes, and sequences isolated from protoplasts. Quantitative real‐time PCR experiments were then carried out using genes representative of different groups. Results of transcript accumulation during protoplast regeneration and sporophyte elicitation supported the hypothesis that specific C5‐epimerase genes are recruited under pathogen attack, enabling L. digitata to modify its cell wall in response to environmental stimuli.
The Use of MoCA and Other Cognitive Tests in Evaluation of Cognitive Impairment in Elderly Patients Undergoing Arthroplasty

Objective: To examine the prevalence and effect of cognitive impairment on treatment outcomes in elderly patients undergoing arthroplasty and to describe the feasibility of cognitive tests. Materials and Methods: The participants were 52 patients with a mean age of 78 years 11 months (SD: 3.3), waiting for primary arthroplasty. We translated Montreal Cognitive Assessment (MoCA) into Finnish and compared it with Mini-Mental State Examination (MMSE), Mini-Cog, and clock-drawing tests prior to and 3 months after the surgery. The ability to perform activities of daily living, depression, quality of life, and years of education were evaluated. Results: The mean MoCA score on the first visit was 20.7 (SD: 4.1). The pre- and postoperative cognitive tests implied there were no changes in cognitive functioning. Unambiguous delirium was detected in 6 patients. Delirium was not systematically assessed and consequently hypoactive delirium cases were possibly missed. Both MMSE and Mini-Cog found 3/6 of those and clock drawing and MoCA 6/6. Low preoperative MoCA, MMSE, and Mini-Cog scores predicted follow-up treatment in health-care center hospitals (P = .02, .011, and .044, respectively). During the 5-year follow-up period, 11/52 patients died. Higher education was the only variable associated with survival. The survivors had attained the median of 8 (range: 4-19) years of education compared with 6 (range: 4-8) years among the deceased. Conclusion: The prevalence of cognitive impairment among older patients presenting for arthroplasty is high and mostly undiagnosed. It is feasible to use the MoCA to identify cognitive impairment preoperatively in this group. The clock-drawing test was abnormal in all patients with postoperative delirium, which could be used as a screening test. Higher education predicted survival on a 5-year follow-up period.