Miracle-dz/UniFAR-FTUs huggingface dataset:
Contralateral breast cancers: Independent cancers or metastases?

A cancer in the contralateral breast in a woman with a previous or synchronous breast cancer is typically considered to be an independent primary tumor. Emerging evidence suggests that in a small subset of these cases the second tumor represents a metastasis. We sought to investigate the issue using massively parallel sequencing targeting 254 genes recurrently mutated in breast cancer. We examined the tumor archives at Memorial Sloan Kettering Cancer Center for the period 1995–2006 to identify cases of contralateral breast cancer where surgery for both tumors was performed at the Center. We report results from 49 patients successfully analyzed by a targeted massively parallel sequencing assay. Somatic mutations and copy number alterations were defined by state‐of‐the‐art algorithms. Clonal relatedness was evaluated by statistical tests specifically designed for this purpose. We found evidence that the tumors in contralateral breasts were clonally related in three cases (6%) on the basis of matching mutations at codons where somatic mutations are rare. Clinical data and the presence of similar patterns of gene copy number alterations were consistent with metastasis for all three cases. In three additional cases, there was a solitary matching mutation at a common PIK3CA locus. The results suggest that a subset of contralateral breast cancers represent metastases rather than independent primary tumors. Massively parallel sequencing analysis can provide important evidence to clarify the diagnosis. However, given the inter‐tumor mutational heterogeneity in breast cancer, sufficiently large gene panels need to be employed to define clonality convincingly in all cases.
Efficacy of Adjuvant S-1 Versus XELOX Chemotherapy for Patients with Gastric Cancer After D 2 Lymph Node Dissection : A Retrospective , Multi-Center Observational Study

Background. After curative resection of gastric cancer with D2 lymph node dissection, postoperative adjuvant chemotherapy with S-1 or capecitabine plus oxaliplatin (XELOX) is considered to be standard therapy in Eastern countries. This study aimed to compare the efficacies of adjuvant S-1 and XELOX chemotherapy for gastric cancer patients after D2 dissection based on disease-free survival (DFS). Methods. This retrospective observational study was conducted at 29 tertiary hospitals in Korea. Of 1898 patients who underwent curative resection and received adjuvant chemotherapy for gastric cancer between February 2012 and December 2013, 1088 patients who met the eligibility criteria were enrolled in the study. After propensity score-matching, the 3-year disease-free survival rate (DFS) was used to compare efficacies directly between adjuvant XELOX and S-1 chemotherapies for patients with stage 2 or 3 gastric cancer after D2 gastrectomy. Results. The 3-year DFS rates for the S-1 and XELOX groups did not differ significantly among disease stages 2A, 2B, and 3A (all p[ 0.05). However, the survival rates for the S-1 group were significantly lower than for the XELOX group for stage 3B (65.8% vs. 68.6%; p = 0.019) and stage 3C (48.4% vs. 66.7%; p = 0.002) gastric cancer. The hazard ratios (HRs) of S-1 chemotherapy for recurrence compared with XELOX for stages 3B and 3C were respectively 2.030 [95% confidence interval (CI), 1.110–3.715; p = 0.022] and 2.732 (95% CI 1.427–5.234; p = 0.002). Conclusions. Adjuvant XELOX chemotherapy was more effective than S-1 for patients with stage 3B or 3C gastric cancer after D2 lymph node dissection. Gastric cancer is the fourth most prevalent cancer and the second most common cause of cancer-related deaths worldwide. Radical gastrectomy with D2 lymphadenectomy is the standard treatment for resectable gastric cancer in an advanced stage. Although radical resection remains the only curative treatment for gastric cancer, recurrence rates are still high, and the patients might die due to disease relapse. Adjuvant chemotherapy has been intensively investigated for several decades and currently is a standard component of resectable gastric cancer therapy because it can improve patient outcomes. Recently, two representative large randomized phase 3 studies have documented the survival benefit of adjuvant chemotherapy for patients with stage 2 or 3 gastric cancer after D2 dissection. The Adjuvant Chemotherapy Trial of TS-1 (ACTS-GC), conducted in Japan, evaluated the Society of Surgical Oncology 2018 First Received: 28 August 2017; Published Online: 15 February 2018 H. Chae, MD, PhD e-mail: hdchae@cu.ac. kr Ann Surg Oncol (2018) 25:1176–1183 https://doi.org/10.1245/s10434-018-6375-z
UvA-DARE ( Digital Academic Repository ) Role of endothelial cell denudation and smooth muscle cell dedifferentiation in neointimal formation of human vein grafts after coronary artery bypass grafting : therapeutic implications

Objective—To provide better insights into the genesis of neointimal thickening in human vein grafts early after surgery. Design—Retrospective study. Setting—Tertiary referral centre. Subjects—18 distal anastomotic sites of patent grafts, obtained at necropsy from eight patients who died over diVering periods (ranging from two days to nine months) after the procedure. Main outcome measures—Immunohistochemical evaluation of smooth muscle cell phenotype modulation in relation to proliferative activity. Results—The earliest changes are characterised by loss of surface lining endothelial cells and insudation of blood corpuscular elements admixed with fibrin-platelet thrombus. At sites of injury vimentin positive and actin negative spindle shaped cells appear in the intima, while the related pre-existent media shows focal absence of actin positive smooth muscle cells. Proliferative activity colocalises at these sites. With time distinct neointimal thickening occurs, associated with disappearance of proliferative activity and a phenotypic shift of the smooth muscle cells. Conclusions—The observation that luminal endothelial cell denudation, with insudation of the intima with blood elements, occurs in the very early stages suggests that these phenomena are responsible for the observed dediVerentiation of pre-existent smooth muscle cells, known to be a prerequisite for cell proliferation and the evolution of intimal thickening. It is likely, therefore, that platelet released growth factors play a pivotal role, which thus may provide a target for preventive pharmacological intervention. (Heart 2000;83:69–75)
Linking late cognitive outcome with glioma surgery location using resection cavity maps

Patients with a diffuse glioma may experience cognitive decline or improvement upon resective surgery. To examine the impact of glioma location, cognitive alteration after glioma surgery was quantified and related to voxel‐based resection probability maps. A total of 59 consecutive patients (range 18–67 years of age) who had resective surgery between 2006 and 2011 for a supratentorial nonenhancing diffuse glioma (grade I–III, WHO 2007) were included in this observational cohort study. Standardized neuropsychological examination and MRI were obtained before and after surgery. Intraoperative stimulation mapping guided resections towards neurological functions (language, sensorimotor function, and visual fields). Maps of resected regions were constructed in standard space. These resection cavity maps were compared between patients with and without new cognitive deficits (z‐score difference >1.5 SD between baseline and one year after resection), using a voxel‐wise randomization test and calculation of false discovery rates. Brain regions significantly associated with cognitive decline were classified in standard cortical and subcortical anatomy. Cognitive improvement in any domain occurred in 10 (17%) patients, cognitive decline in any domain in 25 (42%), and decline in more than one domain in 10 (17%). The most frequently affected subdomains were attention in 10 (17%) patients and information processing speed in 9 (15%). Resection regions associated with decline in more than one domain were predominantly located in the right hemisphere. For attention decline, no specific region could be identified. For decline in information speed, several regions were found, including the frontal pole and the corpus callosum. Cognitive decline after resective surgery of diffuse glioma is prevalent, in particular, in patients with a tumor located in the right hemisphere without cognitive function mapping.
Influenza vaccination challenges in an at-risk student population: considerations for health services

Abstract Background: The American College Health Association’s, National College Health Assessment (ACHA’s NCHA) estimates 46.1% of college students reported being vaccinated in the last year. Objective: 1) To understand the college student’s knowledge, attitude, and beliefs in regards to influenza vaccination; 2) To establish recommendations in a population where high risk transmission does not consistently translate into high vaccination rates. Methods: Utilizing the health belief model (HBM), a cross-sectional study of college student perspectives of influenza vaccination was conducted. Results: Student beliefs regarding vaccination-associated illness and the importance of vaccination did influence vaccination behavior. However, student perceptions of being at risk for the flu and the lack of barriers to vaccination were not found to be significant indicators of vaccination behavior. Conclusion: For this particular population, vaccination promotion efforts may be most effectively targeted in the sophomore and junior years. Findings of this study inform efforts among University Health Services regarding seasonal flu prevention and vaccination on the college campus.
GradNorm: Gradient Normalization for Adaptive Loss Balancing in Deep Multitask Networks

Deep multitask networks, in which one neural network produces multiple predictive outputs, can offer better speed and performance than their single-task counterparts but are challenging to train properly. We present a gradient normalization (GradNorm) algorithm that automatically balances training in deep multitask models by dynamically tuning gradient magnitudes. We show that for various network architectures, for both regression and classification tasks, and on both synthetic and real datasets, GradNorm improves accuracy and reduces overfitting across multiple tasks when compared to single-task networks, static baselines, and other adaptive multitask loss balancing techniques. GradNorm also matches or surpasses the performance of exhaustive grid search methods, despite only involving a single asymmetry hyperparameter $\alpha$. Thus, what was once a tedious search process that incurred exponentially more compute for each task added can now be accomplished within a few training runs, irrespective of the number of tasks. Ultimately, we will demonstrate that gradient manipulation affords us great control over the training dynamics of multitask networks and may be one of the keys to unlocking the potential of multitask learning.
An online survey of tobacco smoking cessation associated with naturalistic psychedelic use

Data suggest psychedelics such as psilocybin and lysergic acid diethylamide (LSD) may hold therapeutic potential in the treatment of addictions, including tobacco dependence. This retrospective cross-sectional anonymous online survey characterized 358 individuals (52 females) who reported having quit or reduced smoking after ingesting a psychedelic in a non-laboratory setting ⩾1 year ago. On average, participants smoked 14 cigarettes/day for 8 years, and had five previous quit attempts before their psychedelic experience. Of the 358 participants, 38% reported continuous smoking cessation after psychedelic use (quitters). Among quitters, 74% reported >2 years’ abstinence. Of the 358 participants, 28% reported a persisting reduction in smoking (reducers), from a mode of 300 cigarettes/month before, to a mode of 1 cigarette/month after the experience. Among reducers, 62% reported >2 years of reduced smoking. Finally, 34% of the 358 participants (relapsers) reported a temporary smoking reduction before returning to baseline smoking levels, with a mode time range to relapse of 3–6 months. Relapsers rated their psychedelic experience significantly lower in personal meaning and spiritual significance than both other groups. Participants across all groups reported less severe affective withdrawal symptoms (e.g. depression, craving) after psychedelic use compared with previous quit attempts, suggesting a potential mechanism of action for psychedelic-associated smoking cessation/reduction. Changes in life priorities/values were endorsed as the most important psychological factor associated with smoking cessation/reduction. Results suggest psychedelics may hold promise in treating tobacco addiction as potentially mediated by spiritual experience, changed priorities/values, and improved emotional regulation.
Skin mechanical properties and modeling: A review

The mechanical properties of the skin are important for various applications. Numerous tests have been conducted to characterize the mechanical behavior of this tissue, and this article presents a review on different experimental methods used. A discussion on the general mechanical behavior of the skin, including nonlinearity, viscoelasticity, anisotropy, loading history dependency, failure properties, and aging effects, is presented. Finally, commonly used constitutive models for simulating the mechanical response of skin are discussed in the context of representing the empirically observed behavior.
Influence of Winter Cover Crop Mulch on Arthropods in a Reduced Tillage Cucurbit System

Abstract Winter cover crop mulches can diversify agricultural habitats and provide a range of benefits for crop production and pest management. Here we report the influence of strip tilled winter cover crop mulches on arthropod abundance in organic vegetable plots. Crookneck squash (Cucurbita pepo L.; Cucurbitales: Cucurbitaceae) was direct seeded into mowed and strip tilled barley (Hordeum vulgare L.; Poales: Poaceae), crimson clover (Trifolium incarnatum L.; Fabales: Fabaceae), a barley + crimson clover mixture, or a no-cover crop control. Arthropods on squash plants were assessed weekly using visual counts. Seed predation was assessed using weed seed arenas. In 2013, mixed species cover crops produced the most ground cover, fewest weeds, and largest squash plants, but herbivore and predator abundance were not correlated with any of those factors. In 2014, mixed species cover crops again produced the most ground cover and fewest weeds, but the largest squash plants were found in no-cover crop control plots, which also had the highest herbivore abundance per plant. Predator and herbivore abundance were positively correlated with squash plant size in 2014. There were no differences in seed predation across treatments. Differences in ground cover biomass and weed presence between the 2 yr may have contributed to differences in squash plant quality and subsequent herbivore abundance between seasons. Results suggest that arthropods on plants responded largely indirectly to cover crops through host plant quality. Results are interpreted in light of overall costs and benefits of cover cropping.
Function and molecular regulation of DWARF1 as a C-24 reductase in brassinosteroid biosynthesis in Arabidopsis

DWARF1 functions as a brassinosteroid C-24 reductase that converts 24-methylene brassinosteroids to 24-methyl brassinosteroids to regulate the endogenous level of an active brassinosteroid, castasterone, to control growth and development in Arabidopsis.
Mineral trioxide aggregate pulpotomy for permanent molars with clinical signs indicative of irreversible pulpitis: a preliminary study

AIM To prospectively investigate the clinical and radiographic success rates of pulpotomy in permanent molars with clinical signs and symptoms suggestive of irreversible pulpitis using mineral trioxide aggregate (MTA) as a pulp dressing agent. METHODOLOGY Sixteen patients with 23 restorable permanent molars exhibiting signs and symptoms indicative of irreversible pulpitis were enrolled. A standardized operative procedure was followed for all participants. All teeth were isolated with a dental dam and caries was removed, and then, pulpotomy performed with a sterile round and/or flame shape diamond burs. Haemostasis was achieved with 5% sodium hypochlorite (NaOCl). A mixture of MTA was placed against the wound, and a moistened cotton pellet was placed over the MTA. Teeth were temporized with a glass-ionomer restoration. Three to ten days later, the interim restoration was removed and setting of MTA was evaluated. Teeth were restored with stainless steel crowns. Follow-up evaluations were scheduled at 3, 6, 12 months and annually thereafter. Descriptive statistics were used to assess outcomes. RESULTS The age of patients at time of pulpotomy ranged between 7.6 and 13.6 years (mean = 10.7± 1.7 yrs). The majority of teeth (91%) had clinical signs and symptoms consistent with a diagnosis of symptomatic irreversible pulpitis and symptomatic apical periodontitis (78%). The follow-up examination period ranged from 18.9 to 73.6 months. Clinically and radiographically, all pulpotomies were considered successful at the end of the follow-up period. Radiographically, a hard tissue barrier was noticed in 13 (57%) teeth. CONCLUSION In children, MTA was associated with high clinical and radiographic success as a pulpotomy agent in permanent teeth with clinical signs and symptoms suggestive of irreversible pulpitis.
Comparative evaluation of blood salvage techniques in patients undergoing cardiac surgery with cardiopulmonary bypass

Background: The primary objective of this study was to test and compare the efficacy of currently available intraoperative blood salvage systems via a demonstration of the level of increase in percentage concentration of red blood cells (RBC), white blood cells 9WBC) and platelets (Plt) in the end product. Methods: In a prospective, randomized study, data of 80 patients undergoing elective cardiac surgery with cardiopulmonary bypass in a 6-month period was collected, of which the volume aspirated from the surgical field was processed by either the HemoSep Novel Collection Bag (Advancis Surgical, Kirkby-in-Ashfield, Notts, UK) (N=40) (Group 1) or a cell- saver (C.A.T.S Plus Autotransfusion System, Fresenius Kabi, Bad Homburg, Germany) (N=40) (Group 2). Results: Hematocrit levels increased from 23.05%±2.7 to 43.02%±12 in Group 1 and from 24.5±2 up to 55.2±9 in Group 2 (p=0.013). The mean number of platelets rose to 225200±47000 from 116400 ±40000 in the HemoSep and decreased from 125200±25000 to 96500±30000 in the cell-saver group (p=0.00001). The leukocyte count was concentrated significantly better in Group 1 (from 10100±4300 to 18120±7000; p=0.001). IL-6 levels (pg/dL) decreased from 223±47 to 83±21 in Group 1 and from 219±40 to 200±40 in Group 2 (p=0.001). Fibrinogen was protected significantly better in the HemoSep group (from 185±35 to 455±45; p=0.004). Conclusions: Intraoperative blood salvage systems functioned properly and the resultant blood product was superior in terms of red blood cell species. The HemoSep group had significantly better platelet and leukocyte concentrations and fibrinogen content.
Fast Convolutional Sparse Coding in the Dual Domain

Convolutional sparse coding (CSC) is an important building block of many computer vision applications ranging from image and video compression to deep learning. We present two contributions to the state of the art in CSC. First, we significantly speed up the computation by proposing a new optimization framework that tackles the problem in the dual domain. Second, we extend the original formulation to higher dimensions in order to process a wider range of inputs, such as RGB images and videos. Our results show up to 20 times speedup compared to current state-of-the-art CSC solvers.
In vitro responses to known in vivo genotoxic agents in mouse germ cells

Genotoxic compounds have induced DNA damage in male germ cells and have been associated with adverse clinical outcomes including enhanced risks for maternal, paternal and offspring health. DNA strand breaks represent a great threat to the genomic integrity of germ cells. Such integrity is essential to maintain spermatogenesis and prevent reproduction failure. The Comet assay results revealed that the incubation of isolated germ cells with n‐ethyl‐n‐nitrosourea (ENU), 6‐mercaptopurine (6‐MP) and methyl methanesulphonate (MMS) led to increase in length of Olive tail moment and % tail DNA when compared with the untreated control cells and these effects were concentration‐dependent. All compounds were significantly genotoxic in cultured germ cells. Exposure of isolated germ cells to ENU produced the highest concentration‐related increase in both DNA damage and gene expression changes in spermatogonia. Spermatocytes were most sensitive to 6‐MP, with DNA damage and gene expression changes while spermatids were particularly susceptible to MMS. Real‐time PCR results showed that the mRNA level expression of p53 increased and bcl‐2 decreased significantly with the increasing ENU, 6‐MP and MMS concentrations in spermatogonia, spermatocytes and spermatids respectively for 24 hr. Both are gene targets for DNA damage response and apoptosis. These observations may help explain the cell alterations caused by ENU, 6‐MP and MMS in spermatogonia, spermatocytes and spermatids. Taken together, ENU, 6‐MP and MMS induced DNA damage and decreased apoptosis associated gene expression in the germ cells in vitro. Environ. Mol. Mutagen. 58:99–107, 2017. © 2017 Wiley Periodicals, Inc.
Room Temperature Multiwavelength Erbium-doped Fiber Laser

An experimental study on the multiwavelength erbium-doped fiber laser is presented.Simultaneous 16 wavelengths operation at room temperature and the length of 4.1 m of birefracting fiber was achieved using an all fiber phase modulator in the erbium-doped fiber ring laser.The fiber laser with the wavelength spacing of 0.8 nm is anchored on the ITU frequency grid.The laser linewidth is less than 0.1 nm with the flat power spectrum.The power fluctuation less than 5 dB spectral width of 12 nm.And the wavelength acing can be adjusted by changing the length of birefracting fiber.
Hearing and seeing meaning in noise: Alpha, beta, and gamma oscillations predict gestural enhancement of degraded speech comprehension

During face‐to‐face communication, listeners integrate speech with gestures. The semantic information conveyed by iconic gestures (e.g., a drinking gesture) can aid speech comprehension in adverse listening conditions. In this magnetoencephalography (MEG) study, we investigated the spatiotemporal neural oscillatory activity associated with gestural enhancement of degraded speech comprehension. Participants watched videos of an actress uttering clear or degraded speech, accompanied by a gesture or not and completed a cued‐recall task after watching every video. When gestures semantically disambiguated degraded speech comprehension, an alpha and beta power suppression and a gamma power increase revealed engagement and active processing in the hand‐area of the motor cortex, the extended language network (LIFG/pSTS/STG/MTG), medial temporal lobe, and occipital regions. These observed low‐ and high‐frequency oscillatory modulations in these areas support general unification, integration and lexical access processes during online language comprehension, and simulation of and increased visual attention to manual gestures over time. All individual oscillatory power modulations associated with gestural enhancement of degraded speech comprehension predicted a listener's correct disambiguation of the degraded verb after watching the videos. Our results thus go beyond the previously proposed role of oscillatory dynamics in unimodal degraded speech comprehension and provide first evidence for the role of low‐ and high‐frequency oscillations in predicting the integration of auditory and visual information at a semantic level.