Miracle-dz/UniFAR-FTUs huggingface dataset:
Non‐chemical inhibition of respiratory motor output during mechanical ventilation in sleeping humans

1 To determine the magnitude and time course of changes in respiratory motor output caused by non‐chemical influences, six sleeping subjects underwent assist‐control mechanical ventilation (ACMV) at increased tidal volume (VT). During ACMV, end‐tidal PCO2 (PET,CO2) was either held at normocapnic levels (PET,CO2, 0·6‐1·1 mmHg > control) by adding CO2 to the inspirate, or it was allowed to fall (hypocapnia). 2 Each sleeping subject underwent several repeat trials of twenty‐five ACMV breaths (VT, 1·3 or 2·1 times control; peak flow rate, 30‐40 l min−1; inspiratory time, ± 0·3 s of control). The end‐tidal to arterial PCO2 difference throughout normocapnic ACMV at raised VT was unchanged from eupnoeic levels during studies in wakefulness. 3 Normocapnic ACMV at both the smaller and larger increases in VT decreased the amplitude of respiratory motor output, as judged by decreased maximum rate of rise of mask pressure (Pm) (mean dPm/dtmax, 46‐68 % of control), reduced diaphragmatic EMG (to 55 % of control) and reduced VT on the first spontaneous breath after ACMV (to 70 % of control). Expiratory time (TE) was slightly prolonged (13‐32 % > control). This inhibition of amplitude of respiratory motor output progressed over the first five to seven ventilator cycles, was maintained over the remaining 18‐20 cycles and persisted for three to five spontaneous breaths immediately following cessation of ACMV. 4 Hypocapnia did not further inhibit respiratory motor output amplitude beyond the effect of normocapnic ACMV at high VT, but did cause highly variable prolongation of TE when PET,CO2 was reduced by greater than 3 mmHg for at least five ventilator cycles. 5 These data in sleeping humans support the existence of a significant, non‐chemical inhibitory influence of ACMV at increased VT and positive pressure upon the amplitude of respiratory motor output; this effect is manifested both during and following normocapnic mechanical ventilation.
Does the guinea‐pig ileum obey the ‘law of the intestine’?

1 We report the first simultaneous mechanical reflex responses of the longitudinal muscle (LM) and circular muscle (CM) layers of the guinea‐pig ileum following mucosal stimulation and distension in vitro. 2 Dissection techniques were used to prevent mechanical interaction between the LM and CM layers both oral and anal to a stimulus site. 3 All graded stimuli produced graded contractions of both the LM and CM orally and anally to the stimulus. Contractions occurred synchronously in the LM and CM and under no circumstances were inhibitory responses recorded in either muscle layer, despite the presence of ongoing cholinergic tone in both the LM and CM. Contractions were abolished by tetrodotoxin (1.6 μm). 4 Local brush stroking of the mucosa evoked a peristaltic wave which readily conducted distally over 13 cm, without the presence of fluid in the lumen. No descending relaxation was observed. 5 Apamin (300 nm) disrupted evoked peristaltic waves and significantly increased the rate‐of‐rise of the LM and CM contractions anal to a stimulus, and the LM oral to a stimulus. 6 N ω‐nitro‐L‐arginine (100 μm), a nitric oxide synthesis inhibitor, had no overall significant effect on the characteristics of the LM and CM contractions, although on occasion an enhancement in their peak amplitude was noted. 7 It is suggested that the guinea‐pig ileum does not conform to the ‘law of the intestine’ as postulated by Bayliss & Starling (1899) . Rather, local physiological stimulation of the ileum elicits a contraction both orally and anally to a stimulus, which occurs synchronously in both the CM and LM layers. Apamin‐sensitive inhibitory neurotransmission modulates the rate‐of‐rise of the anal contraction of the CM, possibly to generate distal propulsion.
Biomedical event extraction via Long Short Term Memory networks along dynamic extended tree

Extracting knowledge from unstructured text is one of the most important goals of Natural Language Processing, especially in biomedical event extraction domain. In this paper, we describe a system for extracting biomedical events among biotope and bacteria from biomedical literature, using the corpus from the BioNLP'16 Shared Task on Bacteria Biotope task. The current mainstream methods for event extraction are based on shallow machine learning methods. However, these methods mainly rely on domain experience and need enormous manual efforts to select features. Therefore, we propose a novel Long Short Term Memory (LSTM) Networks framework DETBLSTM for event extraction. In our framework, a dynamic extended tree is introduced as the input instead of the original sentences, which utilizes the syntactic information. Furthermore, the POS and distance embeddings are added to enrich input information and thus the complex feature extraction can be skipped. In final, we construct a bidirectional LSTM model to extract biomedical events and achieve 57.14% F-score in the test set. Our model obtains a better F-score than all official submissions to BioNLP-ST 2016, which is 1.34% higher than the best system.
Phaseolus acutifolius Lectin Fractions Exhibit Apoptotic Effects on Colon Cancer: Preclinical Studies Using Dimethilhydrazine or Azoxi-Methane as Cancer Induction Agents

Phaseolus acutifolius (Tepary bean) lectins have been studied as cytotoxic molecules on colon cancer cells. The toxicological profile of a Tepary bean lectin fraction (TBLF) has shown low toxicity in experimental animals; exhibiting anti-nutritional effects such as a reduction in body weight gain and a decrease in food intake when using a dose of 50 mg/kg on alternate days for six weeks. Taking this information into account, the focus of this work was to evaluate the effect of the TBLF on colon cancer using 1,2-dimethylhydrazine (DMH) or azoxy-methane/dextran sodium sulfate (AOM/DSS) as colon cancer inductors. Rats were treated with DMH or AOM/DSS and then administered with TBFL (50 mg/kg) for six weeks. TBLF significantly decreased early tumorigenesis triggered by DMH by 70%, but without any evidence of an apoptotic effect. In an independent experiment, AOM/DSS was used to generate aberrant cryptic foci, which decreased by 50% after TBLF treatment. TBLF exhibited antiproliferative and proapoptotic effects related to a decrease of the signal transduction pathway protein Akt in its activated form and an increase of caspase 3 activity, but not to p53 activation. Further studies will deepen our knowledge of specific apoptosis pathways and cellular stress processes such as oxidative damage.
A Clinical, Radiographic and Laboratory Evaluation of Prognostic Factors in 363 Patients with Malignant Pleural Mesothelioma

Background: Malignant pleural mesothelioma (MPM) has a poor prognosis. Objectives: Only few studies in literature investigated the presence of pleural fluid and radiographic findings for the prognosis of MPM. Methods: We retrospectively investigated the hospital charts of 363 MPM patients who were diagnosed from January 1989 to March 2010. Survival time was calculated by the Kaplan-Meier method. Pretreatment clinical, laboratory and radiographic features of each patient at the time of diagnosis were obtained from patients’ charts. Results: The mean age of 363 patients (217 men, 146 women) was 50.6 ± 11.2 years (range 19–85) and the mean survival time was 11.7 ± 8.6 months (range 1–53). Histological types of MPM were epithelial (71.2%), mixed (15.9%) and sarcomatous type (4.9%). The frequency of disease stages were 31.4% for stage 1, 24.2% for stage 2, 28.6% for stage 3 and 15.8% for stage 4. The most frequent symptoms were dyspnea (82.1%), chest pain (68.3%) and weight loss (58.9%). Results of univariate and multivariate analyses revealed that a Karnofsky performance score ≤60, a pleural fluid glucose level ≤40 mg/dl, a C-reactive protein level >50 mg/l, a serum lactate dehydrogenase level >500 U/l, the presence of pleural fluid, pleural thickening >1 cm and a platelet count of >420 × 103/µl were found to be associated with poor prognosis in MPM. Conclusions: Our data suggest that low pleural fluid glucose and high C-reactive protein, the presence of pleural fluid and pleural thickening were associated with poor MPM prognosis. Further prospective studies are needed to highlight prognostic factors more clearly.
Modeling and characterization of a CMOS sensor with surface trenches for high-pressure applications

This paper reports on the systematic characterization and modeling of a CMOS-based sensor for high-pressure applications. The sensor consists of an anodically bonded silicon-glass stack comprising an n-type Wheatstone bridge as the piezoresistive stress-sensing element. Surface trenches introduced into the silicon close to the Wheatstone bridge significantly increase the pressure sensitivity of the device. Pyrex (PX) and SD2 glass substrates are compared in this study with respect to the sensor performance. The sensors were characterized for the first time at temperatures between −40°C and 125°C and hydrostatic pressures up to 600 bar. Experimental results are compared with a theoretical sensor model based on finite element (FE) simulations. The extracted sensitivities at 25°C are 20.7 µV/V/bar and 9.68 µV/V/bar for sensors built on PX and SD2 substrates, respectively. Long-term measurements reveal an insignificant signal drift.
Interpretation of the acetylcholine test of endothelial cell dysfunction in hypertension.

BACKGROUND In the hypertensive circulation, endothelial cells may release less nitric oxide or more endothelin-1, both powerful vasoactive substances, suggesting an attractive hypothesis for the initiation or reinforcement of hypertension. These substances, however, are not the only way that endothelial dysfunction could be involved in hypertension. In this work we examine the role of the endothelium as a diffusion barrier to vasoconstrictor substances, as a metabolic barrier and as a secretory source of paracrine hormones. REVIEW OF DATA The evidence that endothelial cell dysfunction occurs in different forms of hypertension comes mainly from the loss of relaxation revealed by the 'acetylcholine test' in a variety of preparations. We examined the strength of this evidence in terms of the stability of the agonist, equilibrium between agonist and receptor, and variations in acetylcholine and other receptor populations on endothelial and smooth muscle cells. The range (Emax) and sensitivity (EC50) of the acetylcholine test was considered in a novel approach to determine the full range by in vitro assay. Using conscious rabbits, we showed that the vascular amplifier of resistance in the hypertensive bed can lead to misinterpretation of changes in reactivity. CONCLUSION The question of endothelial dysfunction in hypertension as determined by the acetylcholine test is far from proven.
The versatility of the αβ T‐cell antigen receptor

The T‐cell antigen receptor is a heterodimeric αβ protein (TCR) expressed on the surface of T‐lymphocytes, with each chain of the TCR comprising three complementarity‐determining regions (CDRs) that collectively form the antigen‐binding site. Unlike antibodies, which are closely related proteins that recognize intact protein antigens, TCRs classically bind, via their CDR loops, to peptides (p) that are presented by molecules of the major histocompatibility complex (MHC). This TCR‐pMHC interaction is crucially important in cell‐mediated immunity, with the specificity in the cellular immune response being attributable to MHC polymorphism, an extensive TCR repertoire and a variable peptide cargo. The ensuing structural and biophysical studies within the TCR‐pMHC axis have been highly informative in understanding the fundamental events that underpin protective immunity and dysfunctional T‐cell responses that occur during autoimmunity. In addition, TCRs can recognize the CD1 family, a family of MHC‐related molecules that instead of presenting peptides are ideally suited to bind lipid‐based antigens. Structural studies within the CD1‐lipid antigen system are beginning to inform us how lipid antigens are specifically presented by CD1, and how such CD1‐lipid antigen complexes are recognized by the TCR. Moreover, it has recently been shown that certain TCRs can bind to vitamin B based metabolites that are bound to an MHC‐like molecule termed MR1. Thus, TCRs can recognize peptides, lipids, and small molecule metabolites, and here we review the basic principles underpinning this versatile and fascinating receptor recognition system that is vital to a host's survival.
Thermo-mechanical stability and strength of peptide nanostructures from molecular dynamics: self-assembled cyclic peptide nanotubes

Peptide nanostructures present a wide range of opportunities for applications in biomedicine and bionanotechnology; hence experimental and theoretical studies aiming at determination of thermo-mechanical stability of peptide-based nanostructures are critical for the design and development of their technological applications. Here, we present a homogeneous deformation method combined with the finite elasticity theory and molecular dynamics simulations (MD) for the calculation of second-order anisotropic elastic constants for a membrane model made up of self-assembled cyclic peptide nanotubes. We have computed the values of all anisotropic elastic constants at 300 K. The value of the engineering Young’s modulus (in the z direction) is 19.6 GPa. We observed a yield behavior in the z direction for a strain value of 6%. Furthermore, we also report calculated heat capacity, thermal expansion coefficient and isothermal compressibility of the system under study.
Mitogen-activated protein kinase phosphatase-1 inhibition and sustained extracellular signal-regulated kinase 1/2 activation in camptothecin-induced human colon cancer cell death

Camptothecins are commonly used chemotherapeutics; in some models, they enhance signaling via the mitogen-activated protein kinase (MAPK) pathway through effects on upstream kinases. To evaluate the impact of camptothecin (CPT) on MAPKs in human colon cancer, we studied HCT116 and CaCo2 colon cancer cells. We found that HCT116 cells highly express mitogen-activated protein kinase phosphatase-1 (MKP1), which selectively inactivates extracellular signal-regulated kinase (ERK), whereas MKP1 levels were undetectable in CaCo2 cells. CPT did not affect ERK activity in CaCo2 cells, but did induce a striking increase in ERK activity in HCT116 cells in association with a corresponding decrease in MKP1. The reduction in MKP1 expression occurred at a posttranscriptional level and was blocked by the proteasome inhibitor MG132, whereas that CPT-induced downregulation of MKP1 was not due to proteasome-mediated degradation. Treatment of HCT116 cells with CPT induced a sustained activation of nuclear ERK, which was required for CPT-induced apoptosis. P38 and JNK activity were unaffected by CPT, suggesting that the effects of CPT are mediated specifically by ERK. These results suggest that targeting dual-specificity MAPK phosphatases in colon cancer cells may be a viable strategy for optimizing camptothecin-based therapeutic protocols.
Chronic social stress impairs thermal tolerance in the rainbow trout (Oncorhynchus mykiss)

SUMMARY When faced with limited resources, juvenile salmonid fish form dominance hierarchies that result in social stress for socially subordinate individuals. Social stress, in turn, can have consequences for the ability of the fish to respond to additional stressors such as pathogens or exposure to pollutants. In the present study, the possibility that social stress affects the ability of rainbow trout (Oncorhynchus mykiss) to tolerate acute increases in water temperature was investigated. To this end, we first evaluated physiological and cellular stress responses following a 1 h heat shock in juvenile fish in dominance hierarchies. We measured stress hormone (cortisol and catecholamines) concentrations and blood, brain and liver tissue levels of three heat shock proteins (HSPs), the stress inducible HSP70, the constitutive HSC70 and HSP90, in dominant and subordinate trout. No effects of social status on the hormonal response to the heat stress were detected, but the cellular heat shock response in the brain and liver of dominant and subordinate individuals was inhibited. We then assessed thermal tolerance in dominant and subordinate fish through critical thermal maximum temperature (CTmax) trials and measured HSPs following the heat shock. Subordinate fish were less thermally tolerant than their dominant counterparts. We conclude that social stress impacts the ability of fish to respond, on a cellular scale and in a tissue-specific manner, to increases in water temperature, with likely consequences for overall fitness.
Comparative study of ultrasound guided fine needle aspiration cytology with open/laparoscopic biopsy for diagnosis of carcinoma gallbladder.

OBJECTIVE To determine the accuracy of Fine Needle Aspiration Cytology (FNAC) in cases of gallbladder mass. STUDY DESIGN Comparative study. PLACE AND DURATION OF STUDY Surgical Units of Mayo Hospital, Lahore and Lahore General Hospital, Lahore in collaboration with the Department of Radiology, Sir Ganga Ram Hospital, Lahore and Department of Pathology of PGMI, Lahore, from September 2006 to September 2007. METHODOLOGY Ultrasound guided fine needle aspiration cytology was done in all cases and histopathological findings were confirmed with open/laparoscopic biopsies. The results of these two modalities were compared. RESULTS Fifty cases with mean age 60.71+11.073 years presented with mass gallbladder underwent FNAC. Smears showed adenocarcinoma 23, undifferentiated carcinoma in 7, dysplasia and suspicion of malignancy in 5, hemorrhagic background without malignant cells in 12 and inflammatory cells with no malignancy in 3 cases. Results compared with open/ laparoscopic biopsy showed a sensitivity, specificity and Positive Predictive Value (PPV) of 72.91%, 100% and 100% respectively. CONCLUSION Ultrasound guided FNAC is a safe and less invasive diagnostic modality for diagnosing carcinoma gall bladder preventing the patient to undergo major surgery and helps in better quality of life.
Prognostic value of genetic mutations in thyroid cancer: a meta-analysis.

BACKGROUND Genetic mutations have been found to be associated with thyroid cancer. Previous studies have been focused on the relation between genetic mutations and thyroid cancer. We sought to evaluate the prognostic value of the three most common genetic mutations (BRAF, RAS, and RET) in patients with thyroid cancer. METHODS Sources from MEDLINE (inception to December 2013) and EMBASE (inception to December 2013) were searched. Studies of thyroid cancer with results of genetic mutations and studies that reported survival data were included and two authors performed the data extraction independently. Any discrepancies were resolved by a consensus. RESULTS Fourteen studies assessing BRAF mutations, 6 RAS mutations, 4 RET mutations, and 1 with analysis of both BRAF and RAS mutations were included in this meta-analysis. Patients with papillary thyroid cancer with BRAF mutations showed a 1.59-fold higher risk of events or a 2.66-fold higher risk of death than patients with papillary thyroid cancer without a BRAF mutation. Also, patients with RAS mutations showed a 2.90-fold higher risk of death by thyroid cancer than patients without a RAS mutation. In addition, patients with medullary thyroid cancer with RET mutations showed a 5.82-fold higher risk of death by the disease than without a RET mutation. CONCLUSIONS Genetic mutations should be considered as a poor prognostic marker in thyroid cancer and may lead to better management of individual patients. However, the use of genetic mutations as prognostic markers should not be generalized, but individualized in the specific clinic setting.
Different modalities of entry in a large urban clinic in Uganda and impact on outcomes of patients assessing HIV care and treatment

ABSTRACT In resource-limited settings, a number of patients do not receive continuous HIV care. In this analysis, we compared outcomes in patients who entered care by different modality of entry. This was a retrospective analysis of all patients started on antiretroviral treatment (ART) at a large urban center in Uganda from 2005 to 2012. Patients were categorized into three groups (1) Front door: started on ART without interruption during follow-up; (2) drop-out side door: restarted on ART after having an interruption >6 months and (3) transfer-in side door: transferred-in after being started on ART somewhere else. We compared characteristics at enrollment in the three groups and investigated the following outcomes: (1) retention in care (2) switch to second line. In the study period 11,528 (87.2%) were enrolled through the front door, 1159 (8.7%) resumed ART after dropping out, while 527 (4%) patients were transferred in on ART. The three groups were generally comparable, although patients transferred in were sicker. A larger proportion of patients entered through the drop-out side door died or was lost to follow-up (37.3%), as compared to patients in the front door group (24.9%) and transferred-in side door group (17.7%). More patients in the front door group (32.1%) were transferred out during the follow-up. The highest probability of switching to second line was found in the transferred-in group. Patients who re-enter our program after dropping out are at higher risk of dropping out of care and often need to be switched to second-line ART. The high demand for second-line therapy among patients in transfer-in side door reflects failure in management of complicated patients who are usually require “up-transfer” to better treatment centers. In future understanding, the different modes of entry into HIV care will be key in reshaping the general cascade of HIV care.
Spectrum occupancy modeling on the 450 MHz band for cognitive radio application

Currently the spectrum occupancy has been the major concern for regulatory bodies because there are repressed demands of telecommunications users, especially in large cities due to lack of free frequencies. The cognitive radio technology appears on the scene as a solution to improve the spectrum efficiency by increasing the density of users on radio frequencies. However, there are still open issues to optimize techniques for radio spectrum dynamic access, in order to achieve proficiently the spectral vacancy, called white spaces. In this study measurements were performed on various primary users on the 450 MHz band, which is vastly used, in order to understand the spectrum occupancy models. In the research, the captured signals were demodulated and the audio communication was evaluated in order to identify each sequence considered as a conversation, requiring human interpretation. Within each conversation, bursts of audio (speech of interlocutors) were listed. Besides it the spaces between these bursts and the intervals among conversations were recorded as modeling parameters. The results were statistically analyzed and the study proposes to use this data as a basis for developing an algorithm that aims to improve techniques for access the radio spectrum to enable the powerfully utilization of cognitive radios.
Pentoxifylline‐mediated reduction of superoxide anion production by human spermatozoa

Summary. The release of superoxide anions from sperm suspensions prepared for in vitro fertilization was measured by superoxide dismutaseinhibitable reduction of ferricytochrome C in response to phorbol myristate acetate. The superoxide anion production was found to be within the range of 0.21‐3.76 nmoles O‐2 per 106 spermatozoa. Spermatozoa pre‐incubated in the presence of 3.7 or 10 mM of pentoxifylline for 30 min at 37 °C released less (P<0.001) superoxide anions than did the untreated‐control spermatozoa. It has been concluded that the inhibitory effect of pentoxifylline on superoxide anion production may be a factor contributing to the improvement of sperm preparation before insemination, and may, thereby, increase the fertility potential.