Miracle-dz/UniFAR-FTUs huggingface dataset:
A multiphase model for three-dimensional tumor growth

Several mathematical formulations have analyzed the time-dependent behavior of a tumor mass. However, most of these propose simplifications that compromise the physical soundness of the model. Here, multiphase porous media mechanics is extended to model tumor evolution, using governing equations obtained via the thermodynamically constrained averaging theory. A tumor mass is treated as a multiphase medium composed of an extracellular matrix (ECM); tumor cells (TCs), which may become necrotic depending on the nutrient concentration and tumor phase pressure; healthy cells (HCs); and an interstitial fluid for the transport of nutrients. The equations are solved by a finite element method to predict the growth rate of the tumor mass as a function of the initial tumor-to-healthy cell density ratio, nutrient concentration, mechanical strain, cell adhesion and geometry. Results are shown for three cases of practical biological interest such as multicellular tumor spheroids (MTSs) and tumor cords. First, the model is validated by experimental data for time-dependent growth of an MTS in a culture medium. The tumor growth pattern follows a biphasic behavior: initially, the rapidly growing TCs tend to saturate the volume available without any significant increase in overall tumor size; then, a classical Gompertzian pattern is observed for the MTS radius variation with time. A core with necrotic cells appears for tumor sizes larger than 150 μm, surrounded by a shell of viable TCs whose thickness stays almost constant with time. A formula to estimate the size of the necrotic core is proposed. In the second case, the MTS is confined within a healthy tissue. The growth rate is reduced, as compared to the first case—mostly due to the relative adhesion of the TCs and HCs to the ECM, and the less favorable transport of nutrients. In particular, for HCs adhering less avidly to the ECM, the healthy tissue is progressively displaced as the malignant mass grows, whereas TC infiltration is predicted for the opposite condition. Interestingly, the infiltration potential of the tumor mass is mostly driven by the relative cell adhesion to the ECM. In the third case, a tumor cord model is analyzed where the malignant cells grow around microvessels in a three-dimensional geometry. It is shown that TCs tend to migrate among adjacent vessels seeking new oxygen and nutrients. This model can predict and optimize the efficacy of anticancer therapeutic strategies. It can be further developed to answer questions on tumor biophysics, related to the effects of ECM stiffness and cell adhesion on TC proliferation.
Accessory cells in murine Peyer's patch. I. Identification and enrichment of a functional dendritic cell

Previous studies have suggested that in vitro and in vivo immune responses are defective in Peyer's patch (PP) as a result of a deficiency in accessory cell number or function. However, we report here that enzymatic dissociation of PP does release a cell population with accessory activity in oxidative mitogenesis, i.e., the proliferation of periodate-modified T cells. The accessory activity present in PP is quantitatively similar to that of spleen. Accessory function is mediated by a cell type(s) that has the following characteristics: low buoyant density, lack of adherence to plastic or glass surfaces, lack of Fc receptors, and presence of surface Ia and the 33D1 dendritic cell (DC)-specific determinants. This PP accessory cell was markedly enriched by a novel technique. PP cells formed large aggregates when cultured for 16 h with irradiated, periodate-treated spleen cells. From the clusters we obtained a low density cell population that was 60% Ia positive, 33D1 positive, non-T and non-B, Fc receptor-negative, and dendritic in morphology. The DC-enriched populations were 60-80-fold enriched in accessory function relative to unfractionated PP. We can now compare PP accessory cells with accessory cells from other organs, and try to determine how PP dendritic cells contribute to the unique functions of this lymphoid organ.
ULTRAFAST PROCESSES IN BIOLOGY

Recent advances in the generation of subpicosecond pulses (Fork et al., 1981), their amplification (Fork et al., 1982; Migus et al., 1982), and their use in the production of white light continua (Migus et al., 1982a) along with improved time resolution in single-photon counting experiments (Murao et al., 1982; Rigler etal., 1984), for example, have made the study of fast biological processes much more readily accessible. The term “ultrafast” is subject to varied interpretations. In this review, we shall consider these processes which occur on a time scale of 6500 ps to be “ultrafast”. The topics to be discussed can be classified under the general headings of protein dynamics and photosynthesis.
Multicenter phase II trial of gefitinib first-line therapy followed by chemotherapy in advanced non-small-cell lung cancer (NSCLC): SAKK protocol 19/03.

BACKGROUND Gefitinib is active in patients with pretreated non-small-cell lung cancer (NSCLC). We evaluated the activity and toxicity of gefitinib first-line treatment in advanced NSCLC followed by chemotherapy at disease progression. PATIENTS AND METHODS In all, 63 patients with chemotherapy-naive stage IIIB/IV NSCLC received gefitinib 250 mg/day. At disease progression, gefitinib was replaced by cisplatin 80 mg/m(2) on day 1 and gemcitabine 1250 mg/m(2) on days 1, 8 for up to six 3-week cycles. Primary end point was the disease stabilization rate (DSR) after 12 weeks of gefitinib. RESULTS After 12 weeks of gefitinib, the DSR was 24% and the response rate (RR) was 8%. Median time to progression (TtP) was 2.5 months and median overall survival (OS) 11.5 months. Never smokers (n = 9) had a DSR of 56% and a median OS of 20.2 months; patients with epidermal growth factor receptor (EGFR) mutation (n = 4) had a DSR of 75% and the median OS was not reached after the follow-up of 21.6 months. In all, 41 patients received chemotherapy with an overall RR of 34%, DSR of 71% and median TtP of 6.7 months. CONCLUSIONS First-line gefitinib monotherapy led to a DSR of 24% at 12 weeks in an unselected patients population. Never smokers and patients with EGFR mutations tend to have a better outcome; hence, further trials in selected patients are warranted.
Comparative Resistance of Bacterial Foodborne Pathogens to Non-thermal Technologies for Food Preservation

In this paper the resistance of bacterial foodborne pathogens to manosonication (MS), pulsed electric fields (PEFs), high hydrostatic pressure (HHP), and UV-light (UV) is reviewed and compared. The influence of different factors on the resistance of bacterial foodborne pathogens to these technologies is also compared and discussed. Only results obtained under harmonized experimental conditions have been considered. This has allowed us to establish meaningful comparisons and draw significant conclusions. Among the six microorganisms here considered, Staphyloccocus aureus is the most resistant foodborne pathogen to MS and HHP and Listeria monocytogenes to UV. The target microorganism of PEF would change depending on the treatment medium pH. Thus, L. monocytogenes is the most PEF resistant microorganism at neutral pH but Gram-negatives (Escherichia coli, Salmonella spp., Cronobacter sakazakii, Campylobacter jejuni) would display a similar or even higher resistance at acidic pH. It should be noted that, in acidic products, the baroresistance of some E. coli strains would be comparable to that of S. aureus. The factors affecting the resistance of bacterial foodborne pathogens, as well as the magnitude of the effect, varied depending on the technology considered. Inter- and intra-specific differences in microbial resistance to PEF and HHP are much greater than to MS and UV. Similarly, both the pH and aw of the treatment medium highly condition microbial resistance to PEF and HHP but no to MS or UV. Growth phase also drastically affected bacterial HHP resistance. Regarding UV, the optical properties of the medium are, by far, the most influential factor affecting its lethal efficacy. Finally, increasing treatment temperature leads to a significant increase in lethality of the four technologies, what opens the possibility of the development of combined processes including heat. The appearance of sublethally damaged cells following PEF and HHP treatments could also be exploited in order to design combined processes. Further work would be required in order to fully elucidate the mechanisms of action of these technologies and to exhaustively characterize the influence of all the factors acting before, during, and after treatment. This would be very useful in the areas of process optimization and combined process design.
Measurement Errors in Polymerase Chain Reaction Are a Confounding Factor for a Correct Interpretation of 5-HTTLPR Polymorphism Effects on Lifelong Premature Ejaculation: A Critical Analysis of a Previously Published Meta-Analysis of Six Studies

Objective To analyze a recently published meta-analysis of six studies on 5-HTTLPR polymorphism and lifelong premature ejaculation (PE). Methods Calculation of fraction observed and expected genotype frequencies and Hardy Weinberg equilibrium (HWE) of cases and controls. LL,SL and SS genotype frequencies of patients were subtracted from genotype frequencies of an ideal population (LL25%, SL50%, SS25%, p = 1 for HWE). Analysis of PCRs of six studies and re-analysis of the analysis and Odds ratios (ORs) reported in the recently published meta-analysis. Results Three studies deviated from HWE in patients and one study deviated from HWE in controls. In three studies in-HWE the mean deviation of genotype frequencies from a theoretical population not-deviating from HWE was small: LL(1.7%), SL(−2.3%), SS(0.6%). In three studies not-in-HWE the mean deviation of genotype frequencies was high: LL(−3.3%), SL(−18.5%) and SS(21.8%) with very low percentage SL genotype concurrent with very high percentage SS genotype. The most serious PCR deviations were reported in the three not-in-HWE studies. The three in-HWE studies had normal OR. In contrast, the three not-in-HWE studies had a low OR. Conclusions In three studies not-in-HWE and with very low OR, inadequate PCR analysis and/or inadequate interpretation of its gel electrophoresis resulted in very low SL and a resulting shift to very high SS genotype frequency outcome. Consequently, PCRs of these three studies are not reliable. Failure to note the inadequacy of PCR tests makes such PCRs a confounding factor in clinical interpretation of genetic studies. Currently, a meta-analysis can only be performed on three studies-in-HWE. However, based on the three studies-in-HWE with OR of about 1 there is not any indication that in men with lifelong PE the frequency of LL,SL and SS genotype deviates from the general male population and/or that the SL or SS genotype is in any way associated with lifelong PE.
Money for Nothing: Speeding Up Evolutionary Algorithms Through Better Initialization

That the initialization can have a significant impact on the performance of evolutionary algorithms (EAs) is a well known fact in the empirical evolutionary computation literature. Surprisingly, it has nevertheless received only little attention from the theoretical community. We bridge this gap by providing a thorough runtime analysis for a simple iterated random sampling initialization. In the latter, instead of starting an EA with a random sample, it is started in the best of k search points that are taken from the search space uniformly at random. Implementing this strategy comes at almost no cost, neither in the actual coding work nor in terms of wall-clock time. Taking the best of two random samples already decreases the Θ(n log n) expected runtime of the (1+1)~EA and Randomized Local Search on OneMax by an additive term of order √n. The optimal gain that one can achieve with iterated random sampling is an additive term of order √n log n}. This also determines the best possible mutation-based EA for OneMax, a question left open in [Sudholt, IEEE TEC 2013]. At the heart of our analysis is a very precise bound for the maximum of k independent Binomially distributed variables with success probability 1/2.
The Resisted Supination External Rotation Test

Purpose To evaluate a new clinical test, the resisted supination external rotation test, for the diagnosis of superior labral anterior posterior lesions of the shoulder. Study Design Cohort study (diagnosis); Level of evidence, 2. Methods Forty athletes (average age, 23.9 years) with activity-related shoulder pain were enrolled in the study. The patients underwent 3 different tests designed specifically to detect superior labral anterior posterior lesions (the resisted supination external rotation test, the crank test, and the active compression test); the tests were performed in a random order on the affected shoulder. The results of the tests were compared with arthroscopic findings. Results Out of 40 athletes, 29 (72.5%) had superior labral anterior posterior tears. The resisted supination external rotation test had the highest sensitivity (82.8%), specificity (81.8%), positive predictive value (92.3%), negative predictive value (64.3%), and diagnostic accuracy (82.5%) of all tests performed. Conclusion By re-creating the peel-back mechanism, the resisted supination external rotation test is more accurate than 2 other commonly used physical examination tests designed to diagnose superior labral anterior posterior tears in overhead-throwing athletes. By using this test in the context of a thorough clinical history and physical examination, lesions of the superior labrum can be more reliably diagnosed.