Miracle-dz/UniFAR-FTUs huggingface dataset:
Adherence of a Clinical Strain of Mycoplasma fermentans to Human Cultured Epithelial Cells

This study compares the kinetics of adherence of both the prototype strain PG-18 and the recently clinically isolated strain P-140 of Mycoplasma fermentans to HEp-2 cells. M. fermentans may induce respiratory and genitourinary tract infections. We investigated the presence of putative adhesins from strain P-140. A surface protein of 47 kDa, labeled SP47, isolated from M. fermentans P-140, seems to be involved in acterial adherence on HEp-2 cells; this study could allow helping understand the interaction between mycoplasmas and their hosts. Anti-SP47 antibodies inhibited the formation of bacterial clusters and adherence to cultured cells, quantified by ELISA. M. fermentans P-140 was more efficient at adhering to cultured HEp-2 cells than PG-18.
HIV trends in adolescents: tracing our steps in preparation for our future.

To the Editor: I order to provide insights into trends of HIV infection during the 1990s among youth when trend information about HIV was most limited, we assessed the prevalence of HIV among adolescents and young adults, an often overlooked subgroup, from 1992 through 2000, using sentinel HIV surveillance data drawn from the 2 Baltimore City Health Department STD Clinics. We also examined trends in prevalence among 2 important adolescent and young adult risk groups: men who reported same sex activity (MSM) and females reporting partner injection drug use (IDU). Notably very few men or women in this age group reported IDU. For individuals with multiple positive tests, only the first positive test was counted. A total number of 19,597 adolescent and young adults were tested between 1992 and 2000. The population was predominantly male (60%) and black (96%). We found a constantly decreasing trend in positive diagnosis among adolescents between 1992 and 2000, with the rate of positivity declining from 2.34% in 1992 to 0.57% in 2000. The prevalence among MSM declined from 31.25% in 1992 to 10.53% in 2000. Over the same time period, HIV prevalence in females reporting partner IDU decreased from 11.54% to 2.70%. Our results suggest that adolescents and young adults receiving care through the 1990s in 2 Baltimore City STD Clinics had decreasing prevalence of HIV. These results suggest that the true community-level incidence of infection may have been declining in the populations seeking care at the clinic—poorer black men and women. An alternative explanation for these results is that the risk profile of those youth seeking care at the clinic may have changed over time. However, the declining trend in prevalence among patients who were young MSM or young women reporting partner IDU show that even among those young STD Clinic patients at highest risk, prevalence declined. The likelihood that our findings represented a true decrease in HIV incidence are supported by back-calculation estimates of HIV trends.1,2 In both studies, back-calculation estimates suggest that HIV incidence peaked in 1984–1985 and decreased in the early 1990s.1,2 This decline is also supported by Maryland state data that demonstrates a decreasing trend in AIDS cases between 2000 and 2008 which suggests decreasing incidence of HIV during the 1990s.3 Our analysis of data from 2 public STD clinics located in a East Coast city known for high rates of HIV and IDU add support to the belief that the increases in the last decade of the incidence of HIV observed nationally in MSM and women represent true change in the epidemic.1 Future investigations are warranted that examine whether this observed decline in the prevalence of infection during the 1990s occurred in other cities around the United States and to determine which individual and community level factors were associated with the observed change in trajectory of the epidemic in Baltimore over the past 20 years. Such information is essential in developing effective HIV prevention strategies going forward.
Replication of Checkpoints in Recoverable DSM Systems

This paper presents a new technique of recovery for object-based Distributed Shared Memory (DSM) systems. The new technique, integrated with a coherence protocol for atomic consistency model, offers high availability of shared objects in spite of multiple node and communication failures, introducing little overhead. It ensures fast recovery in case of multiple node failures and enables a DSM system to circumvent the network partitioning, as far as a majority partition can be constituted.
Escalated-dose BEACOPP in the treatment of patients with advanced-stage Hodgkin's lymphoma: 10 years of follow-up of the GHSG HD9 study.

PURPOSE The HD9 trial of the German Hodgkin Study Group compared two different doses (baseline and escalated) of the bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone (BEACOPP) chemotherapy regimen in 1,196 patients with advanced-stage Hodgkin's lymphoma (HL). The previous analysis with 5 years median follow-up had indicated improved tumor control with BEACOPP escalated. Since the long-term safety and efficacy of this regimen has been debated, we report the 10-year follow-up. PATIENTS AND METHODS Patients received one of three chemotherapy regimens: eight cycles of cyclophosphamide, vincristine, procarbazine, and prednisone (COPP) alternating with doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD); eight cycles of BEACOPP baseline; or eight cycles of BEACOPP escalated. RESULTS Median follow-up was 111 months. At 10 years, freedom from treatment failure (FFTF) was 64%, 70%, and 82% with OS rates of 75%, 80%, and 86% for patients treated with COPP/ABVD (arm A), BEACOPP baseline (arm B), and BEACOPP escalated (arm C), respectively (P < .001). BEACOPP escalated was significantly better than BEACOPP baseline in terms of FFTF (P < .0001) and OS (P = .0053). A total of 74 second malignancies (6.2%) were documented, including acute myeloid leukemia (0.4%, 1.5%, and 3.0%), non-Hodgkin's lymphoma (2.7%, 1.7%, and 1.0%), and solid tumors (2.7%, 3.4%, and 1.9%). The corresponding overall secondary malignancy rates were 5.7%, 6.6%, and 6.0%, respectively. CONCLUSION The 10-year follow-up of the HD9 trial demonstrates a stabilized significant improvement in long-term FFTF and OS for BEACOPP escalated in advanced-stage HL. These results challenge ABVD as standard of care for this patient population.
Big data and other challenges in the quest for orthologs

Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third ‘Quest for Orthologs’ meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. Availability and implementation: All such materials are available at http://questfororthologs.org. Contact: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac. uk
Isolated bronchial telangiectasia.

Bleeding from telangiectases of the peripheral airways is described in a patient with hemoptysis of two-and-one-half years duration. Fiberoptic bronchoscopy demonstrated many discrete networks of vessels, some of which showed signs of recent bleeding in segmental and subsegmental bronchi. There were no lesions of the skin or other mucosal surfaces, and there was no family history of bleeding. To our knowledge, hemoptysis from telangiectases isolated in the bronchial tree has not been previously described.
The evaluation and comparison of kidney length obtained from axial cuts in spiral CT scan with its true length

Background: Increased size of kidney is the main symptom of pyelonephritis and renal ischemia in children. Ultrasound and computed tomography (CT) scan methods are the imaging methods for evaluating the urogenital system. The aim of this study is to compare the kidney length obtained from spiral CT scan with the true length obtained from multi-slice CT. Materials and Methods: From 100 patients 200 kidneys were examined in Alzahra Hospital in 2012. Multi-slice CT was used to obtain coronal and sagittal cuts to find the length of kidneys. Results: The mean values of true size of axial sections of the right and left kidneys were 108.37 ± 12.3 mm and 109.74 ± 13.6 mm, respectively. The mean difference of axial sections′ lengths in the right and left kidneys was 1.37 ± 1.22 mm. The mean values of length in the spiral CT scan of the right and left kidneys were 98.61 ± 15.8 mm and 103.11 ± 15.9 mm, respectively. The difference in the estimated size by multi-slice CT scan in oblique and axial images was significant (9.77 ± 1.19 mm and 6.63 ± 0.8 mm for the right and left kidneys, respectively (P < 0.001). Conclusion: The average size of both kidneys determined in axial images was smaller than the actual size. The estimation of kidney size in axial images is not reliable, and to obtain the actual size, it is required to have the coronal and sagittal cuts with proper quality, which could be achieved by multi-slice method.
The Effect of Antioxidant Supplementation on Fatigue during Exercise: Potential Role for NAD+(H)

This study compared serum pyridine levels (NAD+ /NADH) in trained (n = 6) and untrained (n = 7) subjects after continuous progressive exercise at 50%, 70% then 95% of physical work capacity until fatigue (TTF) after consuming a placebo or antioxidant (AO) cocktail (Lactaway©). An increase of 17% in TTF was observed in AO as compared to placebo (p = 0.032). This was accompanied by a significant increase in serum NAD+ levels (p = 0.037) in the AO supplemented group post exercise. The increases in NAD+ and improved endurance reflect lower oxidative stress-induced suppression of aerobic respiration.
Implementing High-Performance Geometric Multigrid Solver with Naturally Grained Messages

Structured grid linear solvers often require manually packing and unpacking of communication data to achieve high performance.Orchestrating this process efficiently is challenging, labor-intensive, and potentially error-prone.In this paper, we explore an alternative approach that communicates the data with naturally grained message sizes without manual packing and unpacking. This approach is the distributed analogue of shared-memory programming, taking advantage of the global address space in PGAS languages to provide substantial programming ease. However, its performance may suffer from the large number of small messages. We investigate the runtime support required in the UPC++ library for this naturally grained version to close the performance gap between the two approaches and attain comparable performance at scale using the High-Performance Geometric Multgrid (HPGMG-FV) benchmark as a driver.
Color-gradient lattice Boltzmann modeling of immiscible two-phase flows on partially wetting surfaces

A zero-interfacial-force condition is derived and implemented to improve the wetting boundary scheme for a lattice Boltzmann color-gradient model. This new wetting boundary scheme is validated by two static problems, i.e. a droplet resting on a flat surface and a cylindrical surface, and one dynamic problem, i.e. the capillary filling in a two-dimensional channel. In these simulations, we observe that non-physical mass transfer is suppressed and spurious velocities become smaller. Meanwhile, accurate results including dynamic contact line movement are achieved for a broad range of contact angles. The model is then applied to study the displacement of immiscible fluids in a two-dimensional channel. Both the displacement velocity and the change rate of finger length are found to exhibit a linear dependence on the contact angle at the viscosity ratio of unity. The displacement velocity decreases but the change rate of finger length increases with increasing capillary number, while the displacement velocity tends to be constant, i.e. two-thirds of the maximum inlet velocity, at high viscosity ratios or low capillary numbers. In contrast to the displacement velocity, the change rate of finger length is negligible at high viscosity ratios or low capillary numbers, where the finger length is in an equilibrium state, while the equilibrium finger length itself is smaller at a higher viscosity ratio or a lower capillary number.
Myelinogenesis and Axonal Recognition by Oligodendrocytes in Brain Are Uncoupled in Olig1-Null Mice

Myelin-forming oligodendrocytes facilitate saltatory nerve conduction and support neuronal functions in the mammalian CNS. Although the processes of oligodendrogliogenesis and differentiation from neural progenitor cells have come to light in recent years, the molecular mechanisms underlying oligodendrocyte myelinogenesis are poorly defined. Herein, we demonstrate the pivotal role of the basic helix-loop-helix transcription factor, Olig1, in oligodendrocyte myelinogenesis in brain development. Mice lacking a functional Olig1 gene develop severe neurological deficits and die in the third postnatal week. In the brains of these mice, expression of myelin-specific genes is abolished, whereas the formation of oligodendrocyte progenitors is not affected. Furthermore, multilamellar wrapping of myelin membranes around axons does not occur, despite recognition and contact of axons by oligodendrocytes, and Olig1-null mice develop widespread progressive axonal degeneration and gliosis. In contrast, myelin sheaths are formed in the spinal cord, although the extent of myelination is severely reduced. At the molecular level, we find that Olig1 regulates transcription of the major myelin-specific genes, Mbp, Plp1, and Mag, and suppresses expression of a major astrocyte-specific gene, Gfap. Together, our data indicate that Olig1 is a central regulator of oligodendrocyte myelinogenesis in brain and that axonal recognition and myelination by oligodendrocytes are separable processes.
Designing Antibiotic Cycling Strategies by Determining and Understanding Local Adaptive Landscapes

The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore susceptibility after resistance has arisen have been unsuccessful, including restrictions on prescribing [1] and antibiotic cycling [2], [3]. Part of the problem may be that those efforts have implemented different classes of unrelated antibiotics, and relied on removal of resistance by random loss of resistance genes from bacterial populations (drift). Here, we show that alternating structurally similar antibiotics can restore susceptibility to antibiotics after resistance has evolved. We found that the resistance phenotypes conferred by variant alleles of the resistance gene encoding the TEM β-lactamase (bla TEM) varied greatly among 15 different β-lactam antibiotics. We captured those differences by characterizing complete adaptive landscapes for the resistance alleles bla TEM-50 and bla TEM-85, each of which differs from its ancestor bla TEM-1 by four mutations. We identified pathways through those landscapes where selection for increased resistance moved in a repeating cycle among a limited set of alleles as antibiotics were alternated. Our results showed that susceptibility to antibiotics can be sustainably renewed by cycling structurally similar antibiotics. We anticipate that these results may provide a conceptual framework for managing antibiotic resistance. This approach may also guide sustainable cycling of the drugs used to treat malaria and HIV.
The Influence of Obesity on Prostate Cancer Diagnosis and Treatment

To date there were only a few risk factors for developing prostate cancer (Pca) like advanced age, skin color and family history (Crawford, 2003). For the long time obesity was considered a negative feature which may contribute to chronic diseases like hypertension or diabetes, but its relationship with cancers was unknown. Last years revealed the obvious truth that such relationship exists and may be very strong. The problem seems to be very important given that obesity is very common, especially in western countries. Over the past 25 years, the number of obese men has increased from 15% to 30% in USA. In 2000 66% of adults in U.S were classified as overweight or obese (Flegal et al., 2002) Nowadays no one denies that overweight and obesity is an independent risk factor for developing colon cancer or post-menopausal breast cancer. Relationship with other cancers is still discussed especially in case of Pca. While the connection between obesity and chronic internal diseases is simple to explain, its relation to cancers is not so unequivocal. Most theories indicate the permanent chronic inflammation in obese which may contribute to oncogenesis. Dishormonose observed in obese consists of high levels of insulin, insulin growth factor – 1 (IGF-1) (Chan et al., 1998, 2002), leptin, estrogens, and low levels of androgens. Insulin and IGF -1 are strong mitosis activators which may explain such ”oncopotential”. On the other hand low levels of testosterone and high of estrogen should protect men from developing Pca. It is only a simple example why the relation between obesity and prostate cancer may be very complex.
Phagocytic Receptors Dictate Phagosomal Escape and Intracellular Proliferation of Francisella tularensis

ABSTRACT Francisella tularensis, the causative agent of tularemia, survives and proliferates within macrophages of the infected host as part of its pathogenic strategy, through an intracellular life cycle that includes phagosomal escape and extensive proliferation within the macrophage cytosol. Various in vitro models of Francisella-macrophage interactions have been developed, using either opsonic or nonopsonic phagocytosis, and have generated discrepant results on the timing and extent of Francisella phagosomal escape. Here we have investigated whether either complement or antibody opsonization of the virulent prototypical type A strain Francisella tularensis subsp. tularensis Schu S4 affects its intracellular cycle within primary murine bone marrow-derived macrophages. Opsonization of Schu S4 with either human serum or purified IgG enhanced phagocytosis but restricted phagosomal escape and intracellular proliferation. Opsonization of Schu S4 with either fresh serum or purified antibodies redirected bacteria from the mannose receptor (MR) to the complement receptor CR3, the scavenger receptor A (SRA), and the Fcγ receptor (FcγR), respectively. CR3-mediated uptake delayed maturation of the early Francisella-containing phagosome (FCP) and restricted phagosomal escape, while FcγR-dependent phagocytosis was associated with superoxide production in the early FCP and restricted phagosomal escape and intracellular growth in an NADPH oxidase-dependent manner. Taken together, these results demonstrate that opsonophagocytic receptors alter the intracellular fate of Francisella by delivering bacteria through phagocytic pathways that restrict phagosomal escape and intracellular proliferation.
A Randomized Controlled Trial of Regional Citrate Versus Regional Heparin Anticoagulation for Continuous Renal Replacement Therapy in Critically Ill Adults*

Objective:To determine whether regional anticoagulation of continuous renal replacement therapy circuits using citrate and calcium prolongs circuit life and/or affects circulating cytokine levels compared with regional anticoagulation using heparin and protamine. Design:Multicenter, parallel group randomized controlled trial. Setting:Seven ICUs in Australia and New Zealand. Patients:Critically ill adults requiring continuous renal replacement therapy. Interventions:Patients were randomized to receive one of two methods of regional circuit anticoagulation: citrate and calcium or heparin and protamine. Measurements and Main Results:The primary outcome was functional circuit life measured in hours, assessed using repeated events survival analysis. In addition, we measured changes in interleukin-6, interleukin-8, and interleukin-10 blood levels. We randomized 212 subjects who were treated with 857 continuous renal replacement therapy circuits (median 2 circuits per patient [interquartile range, 1–6], 390 in citrate group vs 467 in heparin group). The groups were well matched for baseline characteristics. Patients receiving regional continuous renal replacement therapy anticoagulation with heparin and protamine were more likely to experience circuit clotting than those receiving citrate and calcium (hazard ratio, 2.03 [1.36–3.03]; p < 0.0005; 857 circuits). The median lifespan of the first study circuit in each patient was 39.2 hours (95% CI, 32.1–48.0 hr) in the citrate and calcium group versus 22.8 hours (95% CI, 13.3–34.0 hr) in the heparin and protamine group (log rank p = 0.0037, 204 circuits). Circuit anticoagulation with citrate and calcium had similar effects on cytokine levels compared with heparin and protamine anticoagulation. There were more adverse events in the group assigned to heparin and protamine anticoagulation (11 vs 2; p = 0.011). Conclusions:Regional citrate and calcium anticoagulation prolongs continuous renal replacement therapy circuit life compared with regional heparin and protamine anticoagulation, does not affect cytokine levels, and is associated with fewer adverse events.
Diamond surface features and metasomatic processes in subcratonic mantle

Natural diamonds show a large diversity of surface dissolution features, some of which develop in the kimberlite magma during ascent whereas others are inherited from the mantle and are preserved due to diamond enclosure within xenoliths. Such mantle-derived dissolution features reflect conditions associated with diamond-destructive metasomatism and help to shed light on metasomatic processes in the subcratonic mantle. Experiments show that the presence and composition of fluid in kimberlite magmas can also radically change diamond surface features. In this study we examine the distribution of mantle-derived resorption features in four diamond parcels from four different lithologies in the BK1 and AK15 kimberlites (Orapa cluster, Botswana). We apply the results of dissolution experiments conducted at mantle conditions, to predict the nature of metasomatic processes in the subcratonic mantle responsible for diamond growth and partial dissolution. The content and nature of nitrogen defects determined by Fourier transform infrared spectroscopy (FTIR) is used to compare the mantle residence conditions of morphologically different diamond groups.