Miracle-dz/UniFAR-FTUs huggingface dataset:
A stromal cell population in the large intestine identified by tissue factor expression that is lost during colorectal cancer progression

Summary Colorectal cancer (CRC) is a major cause of morbidity and mortality, and the composition of the tumour stroma is a strong predictor of survival in this cancer type. Tissue factor (TF) functions as the trigger of haemostasis together with its ligand coagulation factor VII/VIIa, and TF expression has been found in tumour cells of colorectal tumours. However, TF expression in the CRC tumour stroma or its relationship to patient outcome has not yet been studied. To address this question we developed and validated a specific anti-TF antibody using standardised methods within the Human Protein Atlas project. We used this antibody to investigate TF expression in normal colorectal tissue and CRC using immunofluorescence and immunohistochemistry in two patient cohorts. TF was strongly expressed in a cell population immediately adjacent to the colorectal epithelium. These TF-positive cells were ACTA2-negative but weakly vimentin-positive, defining a specific population of pericryptal sheath cells. In colorectal tumours, TF-positive sheath cells were progressively lost after the adenoma-to-carcinoma transition, demonstrating downregulation of this source of TF in CRC. Furthermore, loss of sheath cell TF was significantly associated with poor overall and disease-specific survival in rectal but not colon cancers. In conclusion, we demonstrate that TF is a marker of a specific cell population in the large intestine, which is lost during CRC progression. Our results highlight the role of the tumour stroma in this cancer type and suggest TF to be a potential prognostic biomarker in rectal cancers through the identification of pericryptal sheath cells. Supplementary Material to this article is available online at www.thrombosis-online.com.
Deep-Sequencing Protocols Influence the Results Obtained in Small-RNA Sequencing

Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.
Nicotine Component of Cigarette Smoke Extract (CSE) Decreases the Cytotoxicity of CSE in BEAS-2B Cells Stably Expressing Human Cytochrome P450 2A13

Cytochrome P450 2A13 (CYP2A13), an extrahepatic enzyme mainly expressed in the human respiratory system, has been reported to mediate the metabolism and toxicity of cigarette smoke. We previously found that nicotine inhibited 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) metabolism by CYP2A13, but its influence on other components of cigarette smoke remains unclear. The nicotine component of cigarette smoke extract (CSE) was separated, purified, and identified using high-performance liquid chromatography (HPLC) and ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS), splitting CSE into a nicotine section (CSE-N) and nicotine-free section (CSE-O). Cell viability and apoptosis by Cell Counting Kit-8 (CCK-8) and flow cytometry assays were conducted on immortalized human bronchial epithelial (BEAS-2B) cells stably expressing CYP2A13 (B-2A13) or vector (B-V), respectively. Interestingly, CSE and CSE-O were toxic to BEAS-2B cells whereas CSE-N showed less cytotoxicity. CSE-O was more toxic to B-2A13 cells than to B-V cells (IC50 of 2.49% vs. 7.06%), which was flatted by 8-methoxypsoralen (8-MOP), a CYP inhibitor. CSE-O rather than CSE or CSE-N increased apoptosis of B-2A13 cells rather than B-V cells. Accordingly, compared to CSE-N and CSE, CSE-O significantly changed the expression of three pairs of pro- and anti-apoptotic proteins, Bcl-2 Associated X Protein/B cell lymphoma-2 (Bax/Bcl-2), Cleaved Poly (Adenosine Diphosphate-Ribose) Polymerase/Poly (Adenosine Diphosphate-Ribose) Polymerase (C-PARP/PARP), and C-caspase-3/caspase-3, in B-2A13 cells. In addition, recombination of CSE-N and CSE-O (CSE-O/N) showed similar cytotoxicity and apoptosis to the original CSE. These results demonstrate that the nicotine component decreases the metabolic activation of CYP2A13 to CSE and aids in understanding the critical role of CYP2A13 in human respiratory diseases caused by cigarette smoking.
Stair-Step Pattern of Soil Bacterial Diversity Mainly Driven by pH and Vegetation Types Along the Elevational Gradients of Gongga Mountain, China

Ecological understandings of soil bacterial community succession and assembly mechanism along elevational gradients in mountains remain not well understood. Here, by employing the high-throughput sequencing technique, we systematically examined soil bacterial diversity patterns, the driving factors, and community assembly mechanisms along the elevational gradients of 1800–4100 m on Gongga Mountain in China. Soil bacterial diversity showed an extraordinary stair-step pattern along the elevational gradients. There was an abrupt decrease of bacterial diversity between 2600 and 2800 m, while no significant change at either lower (1800–2600 m) or higher (2800–4100 m) elevations, which coincided with the variation in soil pH. In addition, the community structure differed significantly between the lower and higher elevations, which could be primarily attributed to shifts in soil pH and vegetation types. Although there was no direct effect of MAP and MAT on bacterial community structure, our partial least squares path modeling analysis indicated that bacterial communities were indirectly influenced by climate via the effect on vegetation and the derived effect on soil properties. As for bacterial community assembly mechanisms, the null model analysis suggested that environmental filtering played an overwhelming role in the assembly of bacterial communities in this region. In addition, variation partition analysis indicated that, at lower elevations, environmental attributes explained much larger fraction of the β-deviation than spatial attributes, while spatial attributes increased their contributions at higher elevations. Our results highlight the importance of environmental filtering, as well as elevation-related spatial attributes in structuring soil bacterial communities in mountain ecosystems.
Coral-Segmentation: Training Dense Labeling Models with Sparse Ground Truth

Biological datasets, such as our case of study, coral segmentation, often present scarce and sparse annotated image labels. Transfer learning techniques allow us to adapt existing deep learning models to new domains, even with small amounts of training data. Therefore, one of the main challenges to train dense segmentation models is to obtain the required dense labeled training data. This work presents a novel pipeline to address this pitfall and demonstrates the advantages of applying it to coral imagery segmentation. We fine tune state-of-the-art encoder-decoder CNN models for semantic segmentation thanks to a new proposed augmented labeling strategy. Our experiments run on a recent coral dataset [4], proving that this augmented ground truth allows us to effectively learn coral segmentation, as well as provide a relevant score of the segmentation quality based on it. Our approach provides a segmentation of comparable or better quality than the baseline presented with the dataset and a more flexible end-to-end pipeline.
A Single Cell Extraction Chip Using Vibration-Induced Whirling Flow and a Thermo-Responsive Gel Pattern

We propose a single cell extraction chip with an open structure, which utilizes vibration-induced whirling flow and a single cell catcher. By applying a circular vibration to a micropillar array spiral pattern, a whirling flow is induced around the micropillars, and target cells are transported towards the single cell catcher placed at the center of the spiral. The single cell catcher is composed of a single-cell-sized hole pattern of thermo-responsive gel. The gel swells at low temperatures (≲32 ◦C) and shrinks at high temperatures (≳32 ◦C), therefore, its volume expansion can be controlled by an integrated microheater. When the microheater is turned on, a single cell is trapped by the hole pattern of the single cell catcher. Then, when the microheater is turned off, the single cell catcher is cooled by the ambient temperature. The gel swells at this temperature, and the hole closes to catch the single cell. The caught cell can then be released into culture wells on a microtiter plate by heating the gel again. We conducted single cell extraction with the proposed chip and achieved a 60% success rate, of which 61% cells yielded live cells.
Physiological responses of three species of unionid mussels to intermittent exposure to elevated carbon dioxide

Zones of elevated carbon dioxide (CO2) have been proposed as barriers to fish movements, but impacts of CO2 on non-target sensitive organisms are unknown. In the present study, freshwater mussels were exposed to intermittent elevations in CO2 and showed species-specific mechanisms to regulate acid–base disturbances, along with a stress response.
Universal Definition of Myocardial Infarction: Clinical Insights

Aims: The universal definition of myocardial infarction (MI) classifies acute ischaemia into different classes according to lesion mechanism. Our aim was to perform a detailed comparison between these different types of MI in terms of baseline characteristics, management and prognosis. Methods and Results: An observational retrospective single-centre cohort study was performed, including 1,000 consecutive patients admitted for type 1 (76.4%) or type 2 MI (23.6%). Type 2 MI patients were older, had a higher prevalence of comorbidities and worse medical status at admission. In-hospital mortality did not differ significantly between the MI groups (8.8 vs. 9.7%, p = 0.602). However, mortality during follow-up was almost 3 times higher in type 2 MIs (HR 2.75, p < 0.001). Type 2 MI was an independent all-cause mortality risk marker, adding discriminatory power to the GRACE model. Finally, important differences in traditional risk score performances (GRACE, CRUSADE) were found between both MI types. Conclusions: Several important baseline differences were found between these MI types. Regarding prognosis, long-term survival is significantly compromised in type 2 MIs, potentially translating patients' higher medical complexity and frailty. Distinction between type 1 and type 2 MI seems to have important implications in clinical practice and likely also in the results of clinical trials.
WT1 peptide‐based immunotherapy for advanced thymic epithelial malignancies

Thymic epithelial tumors are rare malignancies, and no optimal therapeutic regimen has been defined for patients with advanced disease. Patients with advanced thymic epithelial tumors, which were resistant or intolerable to prior therapies, were eligible for this study. Patients received 9 mer‐WT1‐derived peptide emulsified with Montanide ISA51 adjuvant via intradermal administration once a week as a monotherapy. After the 3‐month‐protocol treatment, the treatment was continued mostly at intervals of 2–4 weeks until disease progression or intolerable adverse events occurred. Of the 15 patients enrolled, 11 had thymic carcinoma (TC) and 4 had invasive thymoma (IT). Median period from diagnosis to the start of treatment was 13.3 and 65.5 months for TC and IT, respectively. No patients achieved a complete or partial response. Of the 8 evaluable TC patients, 6 (75.0%) had stable disease (SD) and 2 had progressive disease (PD). Of the 4 evaluable IT patients, 3 (75.0%) had SD and 1 (25.0%) had PD. Median period of monotherapy treatment was 133 and 683 days in TC and IT patients, respectively. No severe adverse events occurred during the 3‐month‐protocol treatment. As adverse events in long responders, thymoma‐related autoimmune complications, pure red cell aplasia and myasthenia gravis occurred in two IT patients. Cerebellar hemorrhage developed in a TC patient complicated with Von Willebrand disease. Induction of WT1‐specific immune responses was observed in the majority of the patients. WT1 peptide vaccine immunotherapy may have antitumor potential against thymic malignancies.
Improved Descriptors for Patch Matching and Reconstruction

We propose a convolutional neural network (ConvNet) based approach for learning local image descriptors which can be used for significantly improved patch matching and 3D reconstructions. A multi-resolution ConvNet is used for learning keypoint descriptors. We also propose a new dataset consisting of an order of magnitude more number of scenes, images, and positive and negative correspondences compared to the currently available Multi-View Stereo (MVS) [18] dataset. The new dataset also has better coverage of the overall viewpoint, scale, and lighting changes in comparison to the MVS dataset. We evaluate our approach on publicly available datasets, such as Oxford Affine Covariant Regions Dataset (ACRD) [12], MVS [18], Synthetic [6] and Strecha [15] datasets to quantify the image descriptor performance. Scenes from the Oxford ACRD, MVS and Synthetic datasets are used for evaluating the patch matching performance of the learnt descriptors while the Strecha dataset is used to evaluate the 3D reconstruction task. Experiments show that the proposed descriptor outperforms the current state-of-the-art descriptors in both the evaluation tasks.
Changes in left ventricular strain parameters following pediatric heart transplantation

STE is increasingly utilized to assess strain in a variety of pathologies. Strain measurements have demonstrated utility following HTx and may aid in the detection of rejection and CAV. Strain parameters have not been well defined in the pediatric HTx population. This study aimed to describe strain in pediatric HTx recipients compared to controls and assess changes over time. All pediatric HTx recipients with available echocardiograms (2004‐2015) without rejection or CAV were identified. Longitudinal and circumferential strain was measured at <1 month, 1 year, 3 years, and 5 years post‐transplant and compared to controls. A total of 218 echocardiograms were analyzed in 79 HTx recipients. At <1 month post‐transplant, there was a significant decrement in longitudinal strain (GLS −14.6 vs −19.2, P < .001) with concurrent augmentation of circumferential strain (GCS −27.3 vs −24.3, P = .005). By 1 year post‐HTx, all strain parameters normalized and were not significantly different from the control population. In the absence of graft complications, strain parameters did not change up to 5 years post‐transplant. Abnormal longitudinal strain parameters are present in the early post‐HTx period with a compensatory increase in circumferential strain. These changes normalize by 1 year post‐transplant and do not change over time in the absence of graft complications.
Heartbeat scheduling: provable efficiency for nested parallelism

A classic problem in parallel computing is to take a high-level parallel program written, for example, in nested-parallel style with fork-join constructs and run it efficiently on a real machine. The problem could be considered solved in theory, but not in practice, because the overheads of creating and managing parallel threads can overwhelm their benefits. Developing efficient parallel codes therefore usually requires extensive tuning and optimizations to reduce parallelism just to a point where the overheads become acceptable. In this paper, we present a scheduling technique that delivers provably efficient results for arbitrary nested-parallel programs, without the tuning needed for controlling parallelism overheads. The basic idea behind our technique is to create threads only at a beat (which we refer to as the "heartbeat") and make sure to do useful work in between. We specify our heartbeat scheduler using an abstract-machine semantics and provide mechanized proofs that the scheduler guarantees low overheads for all nested parallel programs. We present a prototype C++ implementation and an evaluation that shows that Heartbeat competes well with manually optimized Cilk Plus codes, without requiring manual tuning.
Influence of continuous rotation or reciprocation of Optimum Torque Reverse motion on cyclic fatigue resistance of nickel‐titanium rotary instruments

AIM To evaluate the resistance to cyclic fatigue of ProTaper Next (PTN; Dentsply Sirona, Ballaigues, Switzerland), Revo-S (Micro-Mega, Besançon, France), Mtwo (Sweden & Martina, Padova, Italy), Twisted Files (TF, SybronEndo, Orange, CA, USA) and EndoWave (J Morita Corporation, Osaka, Japan) used in continuous rotation or in reciprocation of Optimum Torque Reverse motion (OTR). METHODOLOGY A total of 120 nickel-titanium files were tested. Twenty-four instruments for each brand were divided into two groups (n = 12) on the basis of the motion tested: continuous rotation (Group 1) or reciprocation of OTR motion (Group 2). Resistance to cyclic fatigue was determined by recording time to fracture (TtF) in a stainless steel artificial canal with a 60° angle of curvature and 5 mm radius of curvature. The TtF data were analysed by using two-way analysis of variance (anova) and Bonferroni's post hoc tests at 0.05. RESULTS Mtwo and TF had significantly higher TtF when compared with all other instruments, both in continuous rotation and in reciprocation of OTR motion (P < 0.0001 and P < 0.05, respectively). No difference was observed between Mtwo and TF (P > 0.05), in both motions. PTN was associated with higher cyclic fatigue resistance than Revo-S and EndoWave, both in continuous rotation and in reciprocation of OTR motions (P < 0.0001). No difference was observed between Revo-S and EndoWave, in both motions (P > 0.05). Reciprocating OTR motion improved TtF of all instruments (P < 0.0001). CONCLUSIONS Reciprocation of OTR motion improved significantly cyclic fatigue resistance of all instruments tested compared with continuous rotation. Mtwo and TF had significantly higher cyclic fatigue than the other instruments, in both continuous rotation and reciprocation of OTR motion.
High-strength concrete deep beams with effective span and shear span variations

Nineteen reinforced concrete deep beams with compressive strengths in the range of 41 MPa ≤ f' c ≤ 59 MPa (6000 psi ≤ f' c ≤ 8600 psi) were tested under two-point top loading. All the beams were singly reinforced with main steel percentage p = 1.23 percent and with nominal percentage of shear reinforcement ρ v = 0.48 percent. The beams were tested for seven shear span-depth ratios a/d, ranging from 0.27 to 2. 70, and four effective span-depth ratios l e /d, ranging from 2.15 to 5.38. Test results indicate that l e /d has little influence on the magnitude of the failure load. But for beams with a/d ≥ 1.00, the flexural failure mode becomes dominant with increasing l e /d. The test results are compared with predictions based on the current ACI Building Code. The comparisons reported in this paper will provide an added assurance to designers that the deep-beam provisions in the ACI code, though essentially based on concrete strengths of less than 41 MPa (6000 psi) will insure safe designs for higher strength deep beams. However, the ACI code tends to be rather conservative, as shown by comparison to the Deep-Beam Design Guide issued by the Construction Industry Research and Information Association, London. Nevertheless, the ACI code has the important advantage of being easy to use.
1 Latent factors limiting the performance of 2 sEMG-interfaces 3

Recent advances in recording and real-time analysis of surface electromyographic signals 11 (sEMG) have fostered the use of sEMG human-machine interfaces for controlling personal 12 computers, prostheses of upper limbs, and exoskeletons among others. Despite a relatively high 13 mean performance, sEMG-interfaces still exhibit strong variance in the fidelity of gesture 14 recognition among different users. Here we systematically study the latent factors determining the 15 performance of sEMG-interfaces in synthetic tests and in an arcade game. We show that the degree 16 of muscle cooperation and the amount of the body fatty tissue are the decisive factors in synthetic 17 tests. Our data suggest that these factors can only be adjusted by a long-term training, which 18 promotes fine-tuning of low-level neural circuits driving the muscles. A short-term training has no 19 effect on synthetic tests, but significantly increases the game scoring. This implies that it works at a 20 higher decision-making level, not relevant for synthetic gestures. We propose a procedure that 21 enables quantification of the gestures’ fidelity in a dynamic gaming environment. For each 22 individual subject the approach allows identifying “problematic” gestures that decrease gaming 23 performance. This information can be used for optimizing the training strategy and for adapting 24 the signal processing algorithms to individual users, which could be a way for a qualitative leap in 25 the development of future sEMG-interfaces. 26
The Soluble Receptor for Vitamin B12 Uptake (sCD320) Increases during Pregnancy and Occurs in Higher Concentration in Urine than in Serum

Background Cellular uptake of vitamin B12 (B12) demands binding of the vitamin to transcobalamin (TC) and recognition of TC-B12 (holoTC) by the receptor CD320, a receptor expressed in high quantities on human placenta. We have identified a soluble form of CD320 (sCD320) in serum and here we present data on the occurrence of this soluble receptor in both serum and urine during pregnancy. Methods We examined serum from twenty-seven pregnant women (cohort 1) at gestational weeks 13, 24 and 36 and serum and urine samples from forty pregnant women (cohort 2) tested up to 8 times during gestational weeks 17-41. sCD320, holoTC, total TC and complex formation between holoTC and sCD320 were measured by in-house ELISA methods, while creatinine was measured on the automatic platform Cobas 6000. Size exclusion chromatography was performed on a Superdex 200 column. Results Median (range) of serum sCD320 increased from 125 (87-839) pmol/L (week 15) to reach a peak value of 199 (72-672) pmol/L (week 35) then dropped back to its baseline level just before birth (week 40). Around one third of sCD320 was precipitated with holoTC at all-time points studied. The urinary concentration of sCD320 was around two fold higher than in serum. Urinary sCD320/creatinine ratio correlated with serum sCD320 and reached a peak median level of 53 (30–101) pmol/mmol creatinine (week 35). sCD320 present in serum and urine showed the same elution pattern upon size exclusion chromatography. Conclusion We report for the first time that sCD320 is present in urine and in a higher concentration than in serum and that serum and urine sCD320 increase during pregnancy. The high urinary concentration and the strong correlation between urinary and serum sCD320 suggests that sCD320 is filtered in the kidney.