Miracle-dz/UniFAR-FTUs huggingface dataset:
Treatment of stage I and II non-small-cell lung cancer.

BACKGROUND The appropriate staging and treatment of patients with stage I and II non-small-cell lung cancer (NSCLC) are important in that the potential for a lost curative opportunity in this population is greater than for those presenting with advanced NSCLC. METHODS Treatment options -- surgery, radiation therapy, and chemotherapy -- for stage I and II NSCLC are reviewed, and the impact of newer staging modalities on patient survival is discussed, including altering both the lead-time and clinicopathologic stage biases that exist in the diagnosis and treatment of NSCLC. Some predictions are also made regarding how that standard may change for clinicians in the near future, and methods for further improvements in posttreatment survival in this group are discussed. RESULTS Whenever possible, patients with early-stage NSCLC should be treated with surgical resection. Patients for whom resection is not an option may benefit from radiation as definitive therapy. Positive results with neoadjuvant chemotherapy have led to an ongoing randomized trial (Intergroup S9900) to compare surgery alone to neoadjuvant chemotherapy plus surgery. CONCLUSIONS Staging bias may affect the overall low survival of early-stage NSCLC. However, true stage-specific survival may improve with newer imaging modalities. Future advances, including closed transthoracic radiation, thermal ablative therapy techniques, and gene therapy, may supplant the need to surgically resect these tumors to achieve local control.
The Sleeping Brain's Influence on Verbal Memory: Boosting Resistance to Interference

Memories evolve. After learning something new, the brain initiates a complex set of post-learning processing that facilitates recall (i.e., consolidation). Evidence points to sleep as one of the determinants of that change. But whenever a behavioral study of episodic memory shows a benefit of sleep, critics assert that sleep only leads to a temporary shelter from the damaging effects of interference that would otherwise accrue during wakefulness. To evaluate the potentially active role of sleep for verbal memory, we compared memory recall after sleep, with and without interference before testing. We demonstrated that recall performance for verbal memory was greater after sleep than after wakefulness. And when using interference testing, that difference was even more pronounced. By introducing interference after sleep, this study confirms an experimental paradigm that demonstrates the active role of sleep in consolidating memory, and unmasks the large magnitude of that benefit.
Oncology and Chronic Disease

We are pleased to present the chapter on Oncology and Chronic Disease. Most published papers with importance to pediatric endocrinology were about late effects of cancer. This is not surprising since significant improvements in diagnosis and intensive treatment modalities of childhood cancer during the last 20 years have led to increasing survival rates worldwide. In developed countries, 1/250 of the adult population is a long-term survivor of childhood cancer. However, children who survive childhood cancer are at risk of various late effects as young adults, such as second malignant neoplasms, cardiovascular disease, endocrine disorders, and effects on fertility and reproduction. The latter are of particular interest for the surviving patients. Regarding fertility, we selected three guidelines recommending long-term follow-up of survivors. Our impression is that the number of papers published on the topic ‘chronic disease’ in the year 2013 was less than in 2012. As before, we analyzed this topic from two sides: (1) from the perspective of affected patients, e.g. analyzing growth and pubertal development, and (2) from the perspective of side effects on the endocrine system in relation to the respective therapeutic regimens.
Uncertainty and Risk Analysis in Petroleum Exploration and Production

During the past decades, there have been some significant improvements in uncertainty and risk analysis applied to petroleum exploration and pro- duction. This paper presents a brief overview of the main contributions made in the exploration and production stages, followed by a summary of the main trends in the context of an exhaustible resource. Decisions related to pe- troleum exploration and production are still very complex because of the high number of issues involved in the pro- cess. However, uncertainty and risk analysis are becoming more popular as new hardware and software advances appear, contributing in an important manner to clarify the range and the impacts of new discoveries as well as development and production assets.
Gemcitabine and Cisplatin In Metastatic Carcinoma Gallbladder . A Single Institution Retrospective Analysis

BackgroundMetastatic gall bladder cancer (GBC) is an aggressive disease and is often prone to delayed diagnosis. Chemotherapy is the modality most often employed to prolong survival and is superior to best supportive care alone. AimThe aim of this study was to analyse the effect of gemcitabine and cisplatin (G+C) based chemotherapy in metastatic GBC. DesignRetrospective single institution analysis. Material and methodsMedical records of patients with a histopathologic proven diagnosis of metastatic GBC presenting from January 2014 to July 2015 to the department were reviewed, and data were collected from the departmental case files. ResultsTotal number of patients analysed was 25. The median overall survival was 36 weeks (range 3.4-95 weeks). The median time to progression was 20.6 weeks (range 1-82 weeks). 7/25 (28%) patients achieved a complete response, 8/25 (32%) patients had stable disease while 10/25 (40%) patients had progressive disease. The toxicities encountered were chiefly ototoxicity (7.5%), neuropathy (7.5%), anaemia (4.33%) and nauseavomiting (3.5%). ConclusionG+C appears to be a safe and effective regimen for advanced GBC in the subset of patients presenting to our institute. The results achieved by us are comparable to literature.
Methionine Oxidation of Sup35 Protein Induces Formation of the [PSI+] Prion in a Yeast Peroxiredoxin Mutant

The frequency with which the yeast [PSI+] prion form of Sup35 arises de novo is controlled by a number of genetic and environmental factors. We have previously shown that in cells lacking the antioxidant peroxiredoxin proteins Tsa1 and Tsa2, the frequency of de novo formation of [PSI+] is greatly elevated. We show here that Tsa1/Tsa2 also function to suppress the formation of the [PIN+] prion form of Rnq1. However, although oxidative stress increases the de novo formation of both [PIN+] and [PSI+], it does not overcome the requirement of cells being [PIN+] to form the [PSI+] prion. We use an anti-methionine sulfoxide antibody to show that methionine oxidation is elevated in Sup35 during oxidative stress conditions. Abrogating Sup35 methionine oxidation by overexpressing methionine sulfoxide reductase (MSRA) prevents [PSI+] formation, indicating that Sup35 oxidation may underlie the switch from a soluble to an aggregated form of Sup35. In contrast, we were unable to detect methionine oxidation of Rnq1, and MSRA overexpression did not affect [PIN+] formation in a tsa1 tsa2 mutant. The molecular basis of how yeast and mammalian prions form infectious amyloid-like structures de novo is poorly understood. Our data suggest a causal link between Sup35 protein oxidation and de novo [PSI+] prion formation.
Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha)

Indigenous beers (chicha) are part of the indigenous culture in Ecuador. The fermentation process of these beers probably relies on microorganisms from fermented substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava) using bacterial culture and 16S ribosomal RNA (rRNA) gene-based tag-encoded FLX amplicon pyrosequencing (bTEFAP). Surprisingly, we found that Streptococcus salivarius and Streptococcus mutans (part of the human oral microbiota) were among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated that S. salivarius and S. mutans (isolated from these beers) could proliferate in cassava mush. Lactobacillus sp. was predominantly present in most types of Ecuadorian chicha.
Second harmonic generation from ZnO films and nanostructures

Zinc oxide ZnO is a n-type semiconductor having a wide direct band gap (3.37 eV) as well as a non-centrosymmetric crystal structure resulting from hexagonal wurtzite phase. Its wide transparency range along with its second order nonlinear optical properties make it a promising material for efficient second harmonic generation processes and nonlinear optical applications in general. In this review, we present an extensive analysis of second harmonic generation from ZnO films and nanostructures. The literature survey on ZnO films will include some significant features affecting second harmonic generation efficiency, as crystalline structure, film thickness, surface contributes, and doping. In a different section, the most prominent challenges in harmonic generation from ZnO nanostructures are discussed, including ZnO nanowires, nanorods, and nanocrystals, to name a few. Similarly, the most relevant works regarding third harmonic generation from ZnO films and nanostructures are separately addressed. Finally,.
AMP-activated protein kinase controls exercise training- and AICAR-induced increases in SIRT3 and MnSOD

The mitochondrial protein deacetylase sirtuin (SIRT) 3 may mediate exercise training-induced increases in mitochondrial biogenesis and improvements in reactive oxygen species (ROS) handling. We determined the requirement of AMP-activated protein kinase (AMPK) for exercise training-induced increases in skeletal muscle abundance of SIRT3 and other mitochondrial proteins. Exercise training for 6.5 weeks increased SIRT3 (p < 0.01) and superoxide dismutase 2 (MnSOD; p < 0.05) protein abundance in quadriceps muscle of wild-type (WT; n = 13–15), but not AMPK α2 kinase dead (KD; n = 12–13) mice. We also observed a strong trend for increased MnSOD abundance in exercise-trained skeletal muscle of healthy humans (p = 0.051; n = 6). To further elucidate a role for AMPK in mediating these effects, we treated WT (n = 7–8) and AMPK α2 KD (n = 7–9) mice with 5-amino-1-β-D-ribofuranosyl-imidazole-4-carboxamide (AICAR). Four weeks of daily AICAR injections (500 mg/kg) resulted in AMPK-dependent increases in SIRT3 (p < 0.05) and MnSOD (p < 0.01) in WT, but not AMPK α2 KD mice. We also tested the effect of repeated AICAR treatment on mitochondrial protein levels in mice lacking the transcriptional coactivator peroxisome proliferator-activated receptor γ-coactivator 1α (PGC-1α KO; n = 9–10). Skeletal muscle SIRT3 and MnSOD protein abundance was reduced in sedentary PGC-1α KO mice (p < 0.01) and AICAR-induced increases in SIRT3 and MnSOD protein abundance was only observed in WT mice (p < 0.05). Finally, the acetylation status of SIRT3 target lysine residues on MnSOD (K122) or oligomycin-sensitivity conferring protein (OSCP; K139) was not altered in either mouse or human skeletal muscle in response to acute exercise. We propose an important role for AMPK in regulating mitochondrial function and ROS handling in skeletal muscle in response to exercise training.
The indications and outcome of paediatric corneal transplantation in New Zealand: 1991–2003

Aim: To evaluate patient characteristics, indications, surgical details, and outcome of paediatric keratoplasty in New Zealand. Methods: As part of a prospective longitudinal study, paediatric keratoplasty data collected by the New Zealand National Eye Bank (NZNEB) was analysed for the 13 year period 1991–2003. Results: During the study period the NZNEB supplied 2547 corneas for keratoplasty, of which 65 (3%) were used for paediatric patients (14 years or younger). The 65 keratoplasties were performed in 58 eyes of 52 patients (66% male, 34% female, mean age 10.6 years, SD 4.3 years). Indications were classified into three groups: congenital (16%, n = 9), acquired non-traumatic (74%, n = 43), and acquired traumatic (10%, n = 6). Peters’ anomaly (7% of total), keratoconus (67%), and penetrating trauma (8%) were the most common indications in each group, respectively. 82% of keratoplasties with known outcome survived (clear graft) 1 year postoperatively, 16% failed, and one patient died. Keratoplasty for congenital indications had a lower 1 year survival rate (78%) compared to acquired non-traumatic (85%) and traumatic (100%) indications, although the difference was not statistically significant (p = 0.65). 38% of patients with known outcome had a 1 year postoperative best corrected Snellen visual acuity (BCSVA) of 6/9 or better, and 60% had a BCSVA of 6/18 or better. Visual outcome was significantly better for acquired compared to congenital indications (p = 0.03). Conclusion: Analysis of the NZNEB database provided valuable information in relation to paediatric keratoplasty in New Zealand. In particular, this study highlighted an unusually high prevalence of keratoconus as an indication for keratoplasty. In addition, a high 1 year survival rate and good visual outcome were identified, especially in cases of keratoplasty for acquired conditions.
Clinical Diagnosis of Primary Epiploic Appendagitis: Differentiation From Acute Diverticulitis

Background Primary epiploic appendagitis (PEA) is an uncommon cause of abdominal pain that occurs either from appendageal torsion or spontaneous thrombosis of an appendageal draining vein. Primary epiploic appendagitis is frequently misdiagnosed as either appendicitis or diverticulitis, depending on its location. Study Clinical and radiologic characteristics of 8 patients with PEA were retrospectively reviewed and compared with 18 patients with acute diverticulitis. Results Patients with PEA presented with lower abdominal pain of recent onset that was localized to the left (seven cases) and right (one case) lower quadrants. Well-localized tenderness without peritoneal irritation sign was usually the only physical finding. Blood tests were not significant. In acute diverticulitis, the pain was more evenly distributed throughout the lower abdomen and findings like nausea, fever, and leukocytosis were more frequently associated than in PEA. Computed tomography findings, such as pedunculated oval fatty mass with streaky densities connected to the serosal surface of the adjacent colon, can lead to the diagnosis of PEA. Symptoms of PEA were resolved within 1 week (mean, 4.7 days) without surgery. Conclusions When patients with very localized lower abdominal pain and tenderness do not have associated symptoms or laboratory abnormalities, a high index of suspicion for PEA and early radiologic examinations are required.
REVIEW ARTICLE: Sex Hormone Regulation of Innate Immunity in the Female Reproductive Tract: The Role of Epithelial Cells in Balancing Reproductive Potential with Protection against Sexually Transmitted Pathogens

Citation Wira CR, Fahey JV, Ghosh M, Patel MV, Hickey DK, Ochiel DO. Sex hormone regulation of innate immunity in the female reproductive tract: the role of epithelial cells in balancing reproductive potential with protection against sexually transmitted pathogens. Am J Reprod Immunol 2010
Effects of sex and dietary phosphorus level on the apparent metabolizable energy and nutrient digestibility in broiler chickens

The influence of sex of broilers and dietary phosphorus (P) level on energy utilization and apparent ileal digestibility of N, P and phytate-P were investigated. The AMEN was determined using 3- and 6-week old broilers, while the apparent ileal digestibility were determined only with 6-week old birds. Sex of broilers had no effect on the AMEN values determined during week 3. During week 6, the AMEN values for male broilers were higher (P < 0.01) than those for the females. An interaction (P < 0.05) between sex and dietary P level was also observed. AMEN values determined with male broilers were lower in the adequate-P diet compared to those in the low-P diet, whereas no effect of P level was observed in females. Female broilers tended (P < 0.10) to have a higher ileal N digestibility than the males, but a significant (P < 0.01) sex × P level interaction was observed. Males receiving the adequate-P diet had a lower N digestibility than those receiving the low-P diet, whereas the opposite was true in the females. Ileal phytate P degradation in males was higher than in females (0.282 vs. 0.234), but the differences were not significant. Increasing dietary P level increased ileal P digestibility in both the males and females, but the improvements were greater in the females, as indicated by a significant sex × P level interaction.
Comprehensive genomic profiling of pancreatic acinar cell carcinomas identifies recurrent RAF fusions and frequent inactivation of DNA repair genes.

UNLABELLED Pancreatic acinar cell carcinomas (PACC) account for approximately 1% (∼500 cases) of pancreatic cancer diagnoses annually in the United States. Oncogenic therapuetic targets have proven elusive in this disease, and chemotherapy and radiotherapy have demonstrated limited efficacy against these tumors. Comprehensive genomic profiling of a large series of PACCs (n=44) identified recurrent rearrangements involving BRAF and RAF1 (CRAF) in approximately 23% of tumors. The most prevalent fusion, SND1-BRAF, resulted in activation of the MAPK pathway, which was abrogated with MEK inhibition. SND1-BRAF-transformed cells were sensitive to treatment with the MEK inhibitor trametinib. PACCs lacking RAF rearrangements were significantly enriched for genomic alterations, causing inactivation of DNA repair genes (45%); these genomic alterations have been associated with sensitivity to platinum-based therapies and PARP inhibitors. Collectively, these results identify potentially actionable genomic alterations in the majority of PACCs and provide a rationale for using personalized therapies in this disease. SIGNIFICANCE PACC is genomically distinct from other pancreatic cancers. Fusions in RAF genes and mutually exclusive inactivation of DNA repair genes represent novel potential therapeutic targets that are altered in over two thirds of these tumors.
Constitutive overexpression of the contact site A glycoprotein enables growth‐phase cells of Dictyostelium discoideum to aggregate.

The contact site A (csA) glycoprotein is a developmentally regulated cell adhesion molecule which mediates EDTA‐stable cell contacts during the aggregation stage of Dictyostelium discoideum. A transformation vector was constructed which allows overexpression of the csA protein during the growth phase. In that stage the csA protein is normally not expressed; in the transformants it was transported to the cell surface and carried all modifications investigated, including a phospholipid anchor and two types of oligosaccharide chain. csA expression enabled the normal non‐aggregative growth‐phase cells to form EDTA‐stable contacts in suspension and to assemble into three‐dimensional aggregates when moving on a substratum. After prolonged cultivation of csA overexpressing transformants in nutrient medium the developmental program was found to be turned on, as it normally occurs only in starving cells. During later development of transformed cells, the csA glycoprotein remained present on the cell surface, while it is down‐regulated in the wild type. It was detected in both the prestalk and prespore regions of the multicellular slugs made from transformed cells.
Multiple stuck positions actuator faults: A model predictive based reconfigurable control scheme

This paper presents a Fault Tolerant Control scheme for constrained discrete time linear systems against stuck actuators and bounded disturbances. The results here proposed are a significant generalization of a similar algorithm which has been designed only to manage healthy/out-of-service in the actuator units. A first key feature is the capability to exploit existing methods based on polyhedral algebra and computational geometry in order to characterize the reconfiguration logic of the proposed fault tolerant architecture. This is achieved by defining a set of a finite number of piecewise affine systems capable to cover all of the admissible faulty stuck scenario. It is then proved that one-step sequences of controllable sets can be formally defined within a piecewise affine system paradigm under the key property that each region is a polygon.
Criteria are needed for research in vascular depression

There has been longstanding interest in the relationship of depression to vascular disease and this has received renewed interest since the publication of the “vascular depression” hypothesis by Alexopoulos and colleagues (Alexopoulos et al., 1997). They proposed that cerebrovascular disease (CVD) predisposed, precipitated or perpetuated late-life depression by its impact on frontal-subcortical circuits (FSC). However, whilst several lines of research strongly support this proposal, we still have no useful working criteria for vascular depression, assuming such a nosological entity exists.
Learning from Quality Issues of BPMN Models from Industry

Many organizations use business process models to document business operations and formalize business requirements in software-engineering projects. The Business Process Model and Notation (BPMN), a specification by the Object Management Group, has evolved into the leading standard for process modeling. One challenge is BPMN's complexity: it offers a huge variety of elements and often several representational choices for the same semantics. This raises the question of how well modelers can deal with these choices. Empirical insights into BPMN use from the practitioners' perspective are still missing. To close this gap, researchers analyzed 585 BPMN 2.0 process models from six companies. They found that split and join representations, message flow, the lack of proper model decomposition, and labeling related to quality issues. They give five specific recommendations on how to avoid these issues.
CAPTOPRIL MAGNIFIES THE INCREASE IN ANGIOTENSIN I‐CONVERTING ENZYME ACTIVITY IN RATS WITH AMINONUCLEOSIDE NEPHROSIS

1. Serum, tissue and urine angiotensin I‐converting enzyme (ACE) activity was estimated in the following groups of rats: saline‐injected rats (controls); captopril‐treated (CAP) control animals (CONTROL‐CAP); puromycin aminonucleoside (PAN)‐induced nephrotic syndrome (NS); and CAP‐treated animals with NS (NS‐CAP).