Miracle-dz/UniFAR-FTUs huggingface dataset:
Post‐transplant lymphoproliferative disorders: molecular basis of disease histogenesis and pathogenesis

Post‐transplant lymphoproliferative disorders (PTLD) represent a serious complication of solid organ and allogeneic bone marrow transplantation. PTLD generally display B‐cell lineage derivation, involvement of extranodal sites, aggressive histology and clinical behaviour, and frequent association with EBV infection. The occurrence of IgV mutations in the overwhelming majority of PTLD documents that malignant transformation targets germinal centre (GC) B‐cells and their descendants both in EBV–positive and EBV–negative cases. Analysis of phenotypic markers of B‐cell histogenesis, namely BCL6, MUM‐1 and CD138, allows further distinction of PTLD histogenetic categories. PTLD expressing the BCL6+/MUM1+/−/CD138− profile reflect B‐cells actively experiencing the GC reaction and comprise diffuse large B‐cell lymphoma (DLBCL) centroblastic and Burkitt lymphoma. PTLD expressing the BCL6−/MUM1+/CD138− phenotype putatively derive from B‐cells that have concluded the GC reaction and comprise the majority of polymorphic PTLD and a fraction of DLBCL. A third group of PTLD is reminiscent of post‐GC and pre‐ terminally differentiated B‐cells that show the BCL6−/MUM1+/CD138+ phenotype and are morphologically represented by either polymorphic PTLD or DLBCL immunoblastic. The molecular pathogenesis of PTLD involves infection by oncogenic viruses, namely Epstein‐Barr virus, as well as genetic or epigenetic alterations of several cellular genes. At variance with lymphoma arising in immunocompetent hosts, whose genome is relatively stable, a fraction of PTLD are characterized by microsatellite instability as a consequence of defects in the DNA mismatch repair mechanism. Apart from microsatellite instability, molecular alterations of cellular genes recognized in PTLD include alterations of c‐MYC, BCL‐6, p53, DNA hypermethylation, and aberrant somatic hypermutation of proto‐oncogenes. Copyright © 2005 John Wiley & Sons, Ltd.
Amenorrhea and BMI as independent determinants of patient satisfaction in LNG-IUD users: Cross-sectional study in a Central European district

Objective: This study investigated the satisfaction of women carrying the LNG-IUD and determined influencing factors, especially considering bleeding patterns and body mass index (BMI). Design: Cross sectional study. Setting: Gynecological offices in a Central European district. Participants: 1825 women aged between 18 and 60 years. Measurement: While sitting in the waiting room, voluntary patients had to answer a questionnaire about their experiences with the levonorgestrel intrauterine device. One question was used to determine whether the women were current, former or not users of the intrauterine coil. Results: 415 women who had some experiences with Mirena were found. Overall, 266 (65.7%) were “very satisfied,” 83 (20.5%) “quite satisfied,” 18 (4.4%) “moderate satisfied,” 19 (4.7%) “less satisfied,” and the same amount “really not satisfied” with the hormonal coil. Women with amenorrhea were more often “very satisfied” in general, than women with hypermenorrhea (178 (67.9%) vs. 3 (1.1%) p < 0.001). Concerning bleeding patterns, 295 (74.1%) were “very satisfied” and 23 (5.8%) “really not satisfied”. 203 (91.0%) of all amenorrhoeic women were “very satisfied” with their bleeding patterns, but only 2 (9.5%) of all women with hypermenorrhea (p < 0.001 for α = 0.05). Amenorrhea particularly occurred in women who had a significantly lower body mass index (24.4 ± 4.4 kg/m2 vs. 27.6 ± 6.5 kg/m2 in women with hypermenorrhea, p = 0.018 for α = 0.05). After allocating women to the widely used BMI—categories (underweight, normal weight, overweight, obese class I and II) it was evident, that normally weighted women tend toward amenorrhea as well at the beginning of LNG-IUD use as well after 4–5 years of use. In contrast to this, overweighed and obese women tend more often to amenorrhea at the end of use, but not at the beginning (72.7% and 55.6% vs. 25.0% and 0%). Women with a lower BMI were more often “very satisfied” concerning bleeding patterns, but not concerning the general satisfaction. Conclusion: Our study showed much evidence, that amenorrhea occurs more often in women with lower BMI contrary to women with a higher one—especially at the beginning of LNG- IUD use. Furthermore amenorrhea was mostly considered to be a positive menstrual change.
Cardiac surgery in patients with end-stage renal disease on dialysis

Abstract: Objectives. Over the past decade, the number of patients on dialysis and with cardiovascular diseases has steadily increased. This retrospective analysis compares the postoperative mortality after cardiac surgery between patients on hemodialysis and peritoneal dialysis. Methods. Between 1998 and 2015, 136 patients with end-stage renal disease initiating dialysis more than one month before surgery underwent cardiac surgery. Demographics, preoperative hemodynamic and biochemical data were collected from the patient records. Vital status and date of death was retrieved from a national register. Results. Hemodialysis was undertaken in 73% and peritoneal dialysis in 22% of patients aged 59.7 ± 12.9 years, mean EuroSCORE 8.6% ± 3.5. Isolated coronary artery bypass graft was performed in 46%, isolated valve procedure in 29% and combined procedures in 24% with no significant statistical difference between groups. The 30-day mortality was 14% for hemodialysis patients and 3% for peritoneal dialysis patients (p = .056). One-year and 5-year mortality were, 30% and 59% in the hemodialysis group, 30% and 57% in the peritoneal dialysis group (p = .975, p = .852). Independent predictors of total mortality were age (p = .001), diabetes (p = .017) and active endocarditis (p = .012). Conclusion. No statistically significant difference in mortality was found between patients in hemo- or peritoneal dialysis. However, we observed that patients with end-stage renal disease on dialysis have two times higher mortality rate than estimated by EuroSCORE.
Association between Minimal Change Esophagitis and Gastric Dysmotility: A Single-Center Electrogastrography and Endoscopy Study in Children

Purpose Minimal change esophagitis (MCE) is a reflux disease without mucosal breaks, known to be partially associated with abnormal gastric motor function. Electrogastrography (EGG) is commonly applied to assess gastric motor function in a noninvasive fashion. We aimed to determine the relationship between MCE and gastric myoelectrical activity (GME) recorded on EGG in children. Methods We retrospectively assessed the records of 157 children without underlying disease who underwent both EGG and upper gastrointestinal endoscopy at Gachon University Gil Medical Center between January 2010 and June 2015. The children were stratified according to the appearance of the esophagus (normal vs. MCE). Between-group differences in EGG parameters and their correlation with each MCE finding were statistically analyzed. Results Only the power ratio, one of the EGG parameters analyzed, differed significantly between the two groups (MCE, 1.68±3.37 vs. normal, 0.76±1.06; p<0.05), whereas the other parameters, such as dominant frequency, dominant power, and the ratio of abnormal rhythm, showed no differences. Among children with MCE, significant correlations were noted between erythema and power ratio (p<0.05), friability and postprandial dominant frequency (p<0.05), and edema and/or accentuation of mucosal folds and pre-prandial frequency (p<0.05). Helicobacter pylori infection correlated with postprandial arrhythmia (MCE, 33.59±15.52 vs. normal, 28.10±17.23; p<0.05). EGG parameters did not differ between children with normal esophagus and those with biopsy-proven chronic esophagitis. Conclusion In children with MCE, gastric dysmotility may affect the development of MCE, manifesting as EGG abnormalities. H. pylori infection may also affect GME. However, larger prospective investigations are needed to confirm these findings.
Midgap surface states as a novel signature for dxa2-xb2-wave superconductivity.

It is shown that a sizable areal density of midgap states exists on a {110} surface of a ${\mathit{d}}_{\mathit{x}\mathit{a}}^{2}$-${\mathit{x}}_{\mathit{b}}^{2}$-wave superconductor, which can either have vacuum or an insulator at the surface, or be separated from vacuum or an insulator by a clean, size-quantized, normal metal overlayer. These ``midgap'' states have many observable consequences\char22{}some of which are briefly discussed here\char22{}which can be used as a clear signature to distinguish between d-wave and anisotropic s-wave superconductors.
New modes of genetic change in filamentous fungi.

Mendelian genetic analysis of plant pathogenic fungi has been crucial for the discovery of many fundamental principles in plant pathology. The gene-for­ gene hypothesis, for example, an idea essential to understanding host specificity in plant pathogenic fungi, bacteria, and viruses (32), was first articulated by Flor after his exhaustive genetic study of cultivar selectivity in the flax-rust fungus, Melampsora lini (20). More recently, analyses of mei­ otic recombination of traits such as phytoalexin detoxification (99) and mela­ nin biosynthesis (10) in plant pathogenic fungi have confirmed the role of these factors in pathogenicity. However, many important phenomena observed for fungal plant pathogens have never been adequately explained by Mendelian inheritance of pheno­ typic characters. For example, in 1938, Hanson (26) summarized observa­ tions regarding the cultural instability of imperfect plant pathogenic fungi
Evaluating the articulation index for auditory-visual input.

An investigation of the auditory-visual (AV) articulation index (AI) correction procedure outlined in the ANSI standard [ANSI S3.5-1969 (R1986)] was made by evaluating auditory (A), visual (V), and auditory-visual sentence identification for both wideband speech degraded by additive noise and a variety of bandpass-filtered speech conditions presented in quiet and in noise. When the data for each of the different listening conditions were averaged across talkers and subjects, the procedure outlined in the standard was fairly well supported, although deviations from the predicted AV score were noted for individual subjects as well as individual talkers. For filtered speech signals with AIA less than 0.25, there was a tendency for the standard to underpredict AV scores. Conversely, for signals with AIA greater than 0.25, the standard consistently overpredicted AV scores. Additionally, synergistic effects, where the AIA obtained from the combination of different bandpass-filtered conditions was greater than the sum of the individual AIA's, were observed for all nonadjacent filter-band combinations (e.g., the addition of a low-pass band with a 630-Hz cutoff and a high-pass band with a 3150-Hz cutoff). These latter deviations from the standard violate the basic assumption of additivity stated by Articulation Theory, but are consistent with earlier reports by Pollack [I. Pollack, J. Acoust. Soc. Am. 20, 259-266 (1948)], Licklider [J. C. R. Licklider, Psychology: A Study of a Science, Vol. 1, edited by S. Koch (McGraw-Hill, New York, 1959), pp. 41-144], and Kryter [K. D. Kryter, J. Acoust. Soc. Am. 32, 547-556 (1960)].
A normative study of levels of uranium in the urine of British Forces personnel

Objectives: The UK Ministry of Defence (MoD) controls a biological monitoring programme that includes testing for uranium in personnel who served in the conflict in Iraq in 2003. To help interpret the results, the MoD commissioned this study to quantify a normative reference distribution of urinary uranium concentrations in military personnel who had not served in that conflict. Methods: The study selected and visited various military establishments to recruit a representative mix of ranks, genders and occupational groups (combat, support and auxiliary). A standardised protocol and recruitment questionnaire were used. The 125 ml spot urine samples collected were analysed for uranium and creatinine concentrations and (where possible) for uranium isotope 238U/235U ratio. Results: Samples from 732 eligible subjects were analysed. Adjusted uranium concentrations ranged up to 556 ng.g−1 creatinine, somewhat higher than reference values quoted for the USA but much lower than recorded in granite areas such as Finland. Isotope ratio measurements were available for 125 samples (17) with the highest concentrations; these all had a natural isotope signature and no evidence of depleted uranium (DU). On average, urinary uranium concentrations were somewhat lower in officers than in other ranks; they differed also across the services, the Navy being lowest and the Army highest. The levels give no concern regarding health risks in the personnel studied. Conclusion: Since even the highest values were from natural sources, we assume the differences represent differences in ingestion of natural uranium. Definition of a reference distribution or normal values will depend on the subpopulation of interest.
Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome

Significance Fragile X syndrome (FXS) is a frequent mental disorder characterized by intellectual disability and other symptoms including autism. The disease gene-encoded protein FMRP regulates activity-dependent translation of a large number of mRNAs in neurons. We used quantitative mass spectrometry to systematically compare protein expression in neocortical synaptic fractions between Fmr1 (fragile X mental retardation 1) knockout (KO) and wild-type mice during adolescence and adulthood. We discovered an upregulation of a large number of synaptic proteins in young KO mice but not in adult ones. Many of the upregulated proteins are correlated with an increased protein synthesis in KO neurons. This study provides a greatly expanded view of protein-level changes in FXS and identifies a previously unrecognized developmental dynamics in FXS pathogenesis. Fragile X syndrome (FXS) is an X-linked neurodevelopmental disorder characterized by severe intellectual disability and other symptoms including autism. Although caused by the silencing of a single gene, Fmr1 (fragile X mental retardation 1), the complexity of FXS pathogenesis is amplified because the encoded protein, FMRP, regulates the activity-dependent translation of numerous mRNAs. Although the mRNAs that associate with FMRP have been extensively studied, little is known regarding the proteins whose expression levels are altered, directly or indirectly, by loss of FMRP during brain development. Here we systematically measured protein expression in neocortical synaptic fractions from Fmr1 knockout (KO) and wild-type (WT) mice at both adolescent and adult stages. Although hundreds of proteins are up-regulated in the absence of FMRP in young mice, this up-regulation is largely diminished in adulthood. Up-regulated proteins included previously unidentified as well as known targets involved in synapse formation and function and brain development and others linked to intellectual disability and autism. Comparison with putative FMRP target mRNAs and autism susceptibility genes revealed substantial overlap, consistent with the idea that the autism endophenotype of FXS is due to a “multiple hit” effect of FMRP loss, particularly within the PSD95 interactome. Through studies of de novo protein synthesis in primary cortical neurons from KO and WT mice, we found that neurons lacking FMRP produce nascent proteins at higher rates, many of which are synaptic proteins and encoded by FMRP target mRNAs. Our results provide a greatly expanded view of protein changes in FXS and identify age-dependent effects of FMRP in shaping the neuronal proteome.
Organisation and planning of anaesthesia for emergency surgery

Patients presenting for emergency surgery represent a category at high risk of complications, with substantial morbidity and mortality, whose management may be extremely challenging. In this first of two articles we consider the identification and evaluation of high risk emergency patients, the provision of critical care support, the management of sepsis, common postoperative complications and in‐theatre death.
Adenovirus Type 5 E 4 orf 3 Protein Relieves p 53 Inhibition by E 1 B-55-Kilodalton Protein

The E1B-55-kDa protein of adenovirus type 5 and the p53 tumor suppressor gene product form a complex that localizes to the cytoplasm, thereby downregulating p53’s transcriptional activity. The E4orf6 protein binds and relocalizes E1B-55-kDa, and the proteins act synergistically to inactivate p53. We show that another adenovirus E4 gene product, E4orf3, is also sufficient to relocalize E1B-55-kDa from the cytoplasm to the nucleus. Both proteins are then found in discrete nuclear structures (tracks) that are known to contain components of the promyelocytic leukemia-associated nuclear structure. Simultaneously, p53 is dissociated from E1B-55-kDa and is found evenly distributed over the nucleoplasm. In the presence of E4orf3, p53dependent transcriptional activity is no longer repressed by E1B-55-kDa. When E1B-55-kDa is coexpressed with E4orf3 and E4orf6, E1B-55-kDa is found to colocalize with E4orf6 rather than E4orf3. In parallel, p53 is inhibited and degraded by the combination of E1B-55-kDa and E4orf6, regardless of coexpressed E4orf3. This suggests that the effects of E4orf6 on E1B-55-kDa overrule the actions of E4orf3. When cells are infected with virus expressing E4orf3 but not E4orf6, E1B is found in the cell nucleus and p53 enters the virus replication centers. After infection with wild-type adenovirus, E4orf3 is expressed before E4orf6 and E1B temporarily colocalizes with E4orf3 in nuclear tracks before associating with E4orf6. We propose that during adenovirus infection, the E4orf3 protein transiently liberates p53 from its association with E1B-55-kDa. Subsequently, p53 is inactivated and degraded by the combination of E1B-55-kDa and E4orf6.
Contribution of magnetotail reconnection to the cross‐polar cap electric potential drop

[1] Since the work of Dungey (1961), the global circulation pattern with two (dayside and nightside) reconnection regions has become a classic concept. However, the contributions of dayside and nightside sources to the cross-polar cap potential (PCP) are not fully understood, particularly, the relative role and specifics of the nightside source are poorly investigated both in quantitative and qualitative terms. To fill this gap, we address the contributions of dayside and nightside sources to the PCP by conducting global MHD simulations with both idealized solar wind input and an observed event input. The dayside source was parameterized by solar wind–based “dayside merging potential” Φd = LeffVBt sin4(θ/2), whereas to characterize the nightside source we integrated across the tail the dawn-dusk electric field in the plasma sheet (to obtain the “cross-tail potential” Φn). For the idealized run we performed simulations using four MHD codes available at the Community Coordinated Modeling Center to show that contribution of the nightside source is a code-independent feature (although there are many differences in the outputs provided by different codes). Particularly, we show that adding a nightside source to the linear fit function for the ionospheric potential (i.e., using the fit function Φfit = KdΦd + KnΦn + Φ0) considerably improves the fitting results both in the idealized events as well as in the simulation of an observed event. According to these simulations the nightside source contribution to the PCP has a fast response time (<5 min) and a modest efficiency (potential transmission factor from tail to the ionosphere is small, Kn < 0.2), which is closely linked to the primarily inductive character of strong electric field generated in the plasma sheet. The latter time intervals are marked by strongly enhanced nightside (lobe) reconnection and can be associated with substorm expansion phases. This association is further strengthened by the simulated patterns of precipitation, the R1-type field-aligned substorm current wedge currents and Hall electrojet currents, which are consistent with the known substorm signatures.
Probability Models for Optimal Sparing of Distribution Network Transformers

A probabilistic approach for the determination of the optimum number of spare transformers is presented providing minimum annual cost consisting of capital cost for spares and transformer outage costs. The model suggested can cover any transformer unit lifetime and renewal time probability distribution. This makes it possible to account for the effects of transformer deterioration due to aging and to realistically, based upon empirical data, assess the impacts of the renewal time by treating it as a stochastic rather than as a deterministic variable lasting the entire planning period. The comparison of the model presented with the Poisson distribution based approach, widely used in sparing analyses in the past, has shown that the negligence of aging and of the stochastic nature of renewal times can lead to worse than optimal solutions.
Reduced density matrix functional for many-electron systems

Reduced density matrix functional theory for the case of solids is presented and an exchange-correlation functional based on a fractional power of the density matrix is introduced. We show that compared to other functionals, this produces more accurate behavior for total energies as a function of particle number for finite systems. Moreover, it captures the correct band-gap behavior for conventional semiconductors, as well as strongly correlated Mott insulators, where a gap is obtained in the absence of any magnetic ordering.
ASSESSMENT OF PHYLLOPLANE MICRO-ORGANISM POPULATIONS IN CANTERBURY APPLE ORCHARDS

Micro-organism populations on the leaf surface can be an indicator of environmental health in orchards. A method was developed to detect changes in these populations in apple orchards. Firstly, the variation within orchards was investigated by sampling leaves from seven locations within four trees in spring and autumn. The population density and species richness of micro-organisms when grown on PDA showed tree and season effects (P<0.05) but few significant effects of locations within trees or of replicated branches. Based on these findings, the method was modified to study phylloplane micro-organism populations in nine Canterbury orchards at four times during the 1999-2000 season. The method detected an increasing population density and richness (number of recognisable taxonomic units per sample) during the season in all orchards, and higher density and richness (P<0.05) in unconventionally managed orchards compared with conventionally managed orchards.