Miracle-dz/UniFAR-FTUs huggingface dataset:
Breast Cancer in Turkey: Clinical and Histopathological Characteristics (Analysis of 13.240 Patients).

OBJECTIVE Breast cancer is the most common type of cancer and the leading cause of cancer related deaths in women in Turkey, as elsewhere around the world. However, detailed and systematic demographics, data on clinical and pathological characteristics, and treatment were largely unavailable in Turkey until now. This paper is intended to provide an analysis of clinical and pathological data on women registered in the National Breast Cancer Database (Ulusal Meme Kanseri Veri Tabanı [UMKVT]), established within Turkish Federation of Breast Diseases Societies (TMHDF) and available for use in Turkey since 2005. MATERIALS AND METHODS Clinical and pathological data on breast cancer patients registered online in the database from May 01, 2005 to May 01, 2011 were investigated. Parameters examined in patients included age, menopausal status, distribution of clinical and pathological stage, histological type, tumor diameter, histological grades, regional lymphatic stage, estrogen (ER), progesterone (PR), HER-2 receptors and molecular subtypes. Analysis results of these parameters were compared with literature data and discussed. RESULTS A total of 13,240 patients with breast cancer since April 07, 1992 were included in the study, and 99% of them were female. Female breast cancer patients whose requisite parameters had been completely entered in the database were included in the analysis. The mean age was 51.6 years (±12.6; range 12-97), 17% of them were younger than 40 years of age, and 45% were premenopausal. According to an analysis of age groups at diagnosis, the frequency of cancer peaked at the 45 - 49 age group with 16.7%, declining to 7.6% in the 65-69 age group, and then rose again. Most of the patients (78.7%) had invasive ductal, 7.8% were invasive lobular cancers, 9.8% were invasive mixed cancers (invasive ductal + invasive lobular), and 4% were other histological types (e.g. inflammatory, intracystic papillary, mucinous, etc.), respectively. Half of them (50%) had grade III histology. According to an analysis of pathological stages of all breast cancers (stage 0 - IV), 5% were stage 0, 27% were stage I, 44% were stage II, 21% were stage III, and 3% were stage IV breast cancer, respectively. The mean tumor diameter was 2.5 cm (±1.6; range 0.1-20 cm). The rates of lymphatic stages were pN0 50%, pN1 28%, pN2 15%, and pN3 7%, respectively. ER, PR, and HER-2 receptors were positive in 70%, 59%, and 23% of patients. A subtype analysis of tumors showed that 62% were type luminal A. This was followed by subtypes luminal B (15%), triple negative (15%), and HER-2 positive (8.5%). CONCLUSION As a conclusion patients with breast cancer in our breast cancer registry program were younger, and had more advanced disease, and worse prognostic factors than patients in developed countries.
Dynamic Re-Composition of Learning Groups Using PSO-Based Algorithms

In collaborative learning contexts, the problem of automatically forming effective learning groups gets considerably complex with larger class sizes, e.g. in MOOCs. Additionally, group dynamics caused by high dropout rates currently observable on online open course platforms poses challenges to learning group formation strategies. To address these problems, this paper presents PSO-based algorithms to dynamically re-compose learning groups. In addition to static grouping criteria (such as MBTI personality types), the algorithms take into account factors of the group success rate and group satisfaction during re-composition. We carried out simulations based on randomly generated sample data. The experimental results show that the proposed approach performs better than traditional exhaustive or random methods.
Lignin-Derived Carbon Fiber as a Co-Product of Refining Cellulosic Biomass

Lignin by-products from biorefineries has the potential to provide a low-cost alternative to petroleum-based precursors to manufacture carbon fiber, which can be combined with a binding matrix to produce a structural material with much greater specific strength and specific stiffness than conventional materials such as steel and aluminum. The market for carbon fiber is universally projected to grow exponentially to fill the needs of clean energy technologies such as wind turbines and to improve the fuel economies in vehicles through lightweighting. In addition to cellulosic biofuel production, lignin-based carbon fiber production coupled with biorefineries may provide $2,400 to $3,600 added value dry Mg-1 of biomass for vehicle applications. Compared to producing ethanol alone, the addition of lignin-derived carbon fiber could increase biorefinery gross revenue by 30% to 300%. Using lignin-derived carbon fiber in 15 million vehicles per year in the US could reduce fossil fuel consumption by 2-5 billion liters year-1, reduce CO2 emissions by about 6.7 million Mg year-1, and realize fuel savings through vehicle lightweighting of $700 to $1,600 per Mg biomass processed. The value of fuel savings from vehicle lightweighting becomes economical at carbon fiber price of $6.60 kg-1 under current fuel prices, or $13.20 kg-1 undermore » fuel prices of about $1.16 l-1. « less
Cadmium: Toxicity effect and its mechanism

Cadmium is a heavy metal thatoccurs as a natural constituent in earth’s crust along with Copper, Lead, Nickel and Zinc. Cadmium is vastly used in batteries, coating, plating, alloys etc. in various industries. Humans arecommonly exposed to cadmium by inhalation and ingestion through Cigarettes, Batteries and other factors. Cadmium enters inair and bind to small particles where it can combine with water or soil causing contaminationof fish, plants and animals. Spills at hazardous waste sites and improper waste disposalcan cause cadmium leakages in nearby habitats. Foodstuffs like liver, mushrooms, shellfish, mussel, cocoa powder and dried seaweed are cadmium rich increasing the concentration in human bodies. Cigarettes contains tobacco smoke that transports cadmium into lungs and then to the rest of the body through blood. Bioaccumulation of cadmium in human body and in food chain leads to acute and chronic intoxications. Health effects includes Diarrhea, stomach pains, Bone fracture, Reproductive failure and possibly even infertility, Damage to the central nervous system and immune system, Psychological disorders, etc. Cadmium can also cause the transformation of normal epithelial cells into carcinogenic cells by inhibiting the biosynthesis of protein.Cadmium waste streams from the industries end up in soil which can pollute both soil and surface water. The organic matter in the soil absorbs cadmium increasing the risk of survival of various plants and also increases the uptake of this toxic metal in food. This review is about the study of toxicity mechanism of cadmium in human beings and plants and the biological phenomena involved.
Development and validation of a spectral library searching method for peptide identification from MS/MS

A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time‐consuming and error‐prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open‐source, functionally complete, high‐throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high‐quality spectral library was constructed by combining the high‐confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30 000 spectra for Saccharomyces cerevisiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteomic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.
Design of a fretting fatigue test rig with compliant springs

Fretting is a small amplitude oscillatory movement which occurs between contacting bodies who are subjected to cyclic loading or vibrations. In the contact area arise stresses -normal and tangential- causing stress concentrations and surface degradation. Fretting in combination with ordinary fatigue will reduce the plain fatigue lifetime due to the additional stresses and surface degradation. Applications susceptible to fretting fatigue are for instance connections techniques. By nature they have contacting bodies and transfer loads or vibrations. Connection techniques commonly seen in the field of fretting fatigue are lap-joints, dovetail connections and spline connections. Although mitigating or managing fretting fatigue is industrially relevant, academic research is confined and only revealed basic insights. Therefore, we developed a fretting fatigue test rig at Soete Laboratory. The paper describes the design of the test rig and points out some important features. To study the general phenomenon of fretting fatigue we selected a coupon scale test rig rather than a full scale test rig where only one application can be studied. The specimens used are one dog bone specimen and two indentation pads which make contact with the dog bone specimen. The normal force FN between the specimen and the pads is close loop controlled with a hydraulic actuator. A second hydraulic actuator controls the dynamic force Ffat in the dog bone specimen. A third force FT is introduced during dynamic loading between the dog bone specimen and the pads by means of compliant springs. The combination of these three forces: FN, Ffat, FT in the contact area gives rise to the fretting fatigue phenomenon. The test rig at Soete laboratory can be used to study fretting fatigue and examine mitigations such as surface texturing, surface work hardening, etc.
Increased Cellular Senescence and Vascular Rarefaction Exacerbate the Progression of Kidney Fibrosis in Aged Mice Following Transient Ischemic Injury

Recent findings indicate that elderly patients with acute kidney injury (AKI) have an increased incidence of progression to chronic kidney disease (CKD) due to incomplete recovery from an acute insult. In the current study, a co-morbid model of AKI was developed to better mimic the patient population and to investigate whether age exacerbates the fibrosis and inflammation that develop in the sequelae of progressive kidney disease following acute injury. Young (8–10 weeks) and aged (46–49 weeks) C57BL/6 mice were subjected to 30 min bilateral renal ischemia-reperfusion (I/R) to induce AKI. The aged animals have greater mortality and prolonged elevation of plasma creatinine correlating with less tubular epithelial cell proliferation compared to the young. Six weeks post-reperfusion, interstitial fibrosis is greater in aged kidneys based on picrosirius red staining and immunolocalization of cellular fibronectin, collagen III and collagen IV. Aged kidneys 6 weeks post-reperfusion also express higher levels of p53 and p21 compared to the young, correlating with greater increases in senescence associated (SA) β-galactosidase, a known marker of cellular senescence. A higher influx of F4/80+ macrophages and CD4+ T lymphocytes is measured and is accompanied by increases in mRNA of monocyte chemoattractant protein-1 (MCP-1) and tumor necrosis factor-α (TNF-α). Importantly, microvascular density is significantly less, correlating with an increase in nitro-tyrosine, a marker of oxidative stress. Collectively, these data demonstrate that prolonged acute injury in the aged animals results in an accelerated progression of kidney disease in a chronic state.
Effects of cigarette smoking on the immune system: Follow‐up studies in normal subjects after cessation of smoking

Previous reports of an association between cigarette smoking and the depression of immune function were investigated by studies of 35 subjects before, and three months after, they had ceased to smoke cigarettes. The studies included tests of natural killer cell (NK) activity against several target ceUs and the measurement of immunoglobulin levels in sera and saliva. Similar tests were conducted on 29 control subjects who continued to smoke. THe results indicated a' significant decrease in lymphocyte counts and a significant increase in NK activity against cultured melanoma cells in subjects who ceased smoking. Serum IgG and IgM levels rose significantly in those who ceased smoking cigarettes, but there was no change in IgA levels. Similar increases in immunoglobulin levels (lgA and IgG) in mucosal secretions (saliva) were . noted after cessation of smoking. The NK activity and immunoglobulin levels of smokers who continued to smoke did not show significant changes. These results were consistent with the reversal of changes in immune function associated with smoking. We suggest that these findings may provide further insight into the association of smoking with an increased incidence of certain malignant diseases and respiratory infections.
Randomly amplified polymorphic DNA (RAPD) for rapid typing of Lactobacillus plantarum strains

Randomly amplified polymorphic DNA (RAPD) has been used for rapid typing of Lactobacillus plantarum strains. RAPD was used with either purified chromosomal DNA serving as template in the polymerase chain reaction, or with crude cell extracts, and using a 9‐mer primer with 80% G + C content. Amplified DNA was visualized by ethidium bromide staining after separation on agarose gels. Patterns from 20 Lact. plantarum strains and two Lact. pentosus strains were analysed using the Pearson products moment correlation coefficient (r) and the unweighted pair group method with arithmetic averages (UPGMA). With some exceptions, the two sources of template DNA gave the same clusters and subclusters of strains at the similarity level of 50%. About 50% of the strains could be individually separated from all the other tested strains. The buffer brand, the amount of primer and crude cell extract used in the PCR‐step were crucial for the final pattern.
Amitriptyline enhances the central component of physiological tremor

OBJECTIVES Postural tremor is a regularly encountered side effect of amitriptyline which can be strong enough to cause discontinuation of therapy. The aim was to characterise amitriptyline induced tremor and to assess if the central or reflex component of physiological tremor was modulated by this drug. METHODS The postural hand tremor was measured in 15 patients on a clinical rating scale, by power spectral analysis of accelerometer, forearm flexor, and extensor EMG before and after the beginning of amitriptyline treatment for major depression or chronic pain syndrome. A coherence analysis between flexor and extensor muscles on the same side was performed. RESULTS There was a clinically visible increase in postural tremor in a third of these patients. The tremor amplitude measured by accelerometer total power increased in every patient under amitriptyline. The EMG synchronisation as reflected by significant peaks in the flexor or extensor spectrum generally occurring at higher frequencies (8–18 Hz) than the accelerometric tremor frequencies (6–11 Hz) did not change. The number of patients with a significant flexor-extensor coherence in the 7–15 Hz range increased significantly under amitriptyline, the frequency bands of significant coherence corresponded with the EMG frequencies, and both were independent of changes to the hand's resonant frequency by added inertia. CONCLUSIONS An enhancement of postural tremor under amitriptyline is a common phenomenon although not always clinically apparent. The increase in EMG-EMG coherence indicates an increased common central drive to the motor units as its frequency is not influenced by peripheral resonance or reflex mechanisms. This is the first account of a drug induced enhancement of the central component of physiological tremor.
Compatibility verification for Web service choreography

In this paper we discuss a model-based approach to verifying process interactions for coordinated Web service compositions. The approach uses finite state machine representations of Web service orchestrations and assigns semantics to the distributed process interactions. The move towards implementing Web service compositions by multiple interested parties as a form of distributed system architecture motivates the need for supporting compatibility verification of activities and transactions in all the processes. The described approach is supported by a suite of cooperating tools for specification, formal modeling and providing verification results from orchestrated Web service interactions.
Stress-induced Ethylene Production in the Ethylene-requiring Tomato Mutant Diageotropica.

Ethylene synthesis in vegetative tissues is thought to be controlled by indoleacetic acid (IAA). However, ethylene synthesis in the diageotropica (dgt) mutant of tomato (Lycopersicon esculentum Mill.) was much less sensitive to IAA than in the normal variety (VFN8). Yet, mechanical wounding stimulated ethylene production by the mutant. The dgt tomato provides an opportunity to study the regulation of stress ethylene independent of IAA effects. Waterlogging (i.e. anaerobic stress) stimulated production of the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), in the roots. The ACC was transported to the shoot where it was converted to ethylene. The dgt mutant efficiently utilized ACC for ethylene synthesis under aerobic conditions. The results confirm that the genetic lesion in dgt is located at a step prior to the formation of ACC. Furthermore, induction of ethylene synthesis by anaerobic or mechanical stresses in this mutant is independent of IAA action.
Characterization of Hybrid-Wicked Copper Heat Pipe

Thermal management of high power electronics is becoming a critical issue as the power density of semiconductors increasing. The flat heat pipe (FHP) is widely used in the electronic cooling because it is possible to interface with flat electronics packages without additional conductive and interface resistances. The heat flux of the next generation electronics may exceed 100 W/cm2 , which is significantly beyond the cooling capabilities of commercially available FHP today. A novel micro scale hybrid wick was developed in this study to improve the effective thermal conductivity and working heat flux of FHP. The hybrid wick consists of multilayer of sintered copper woven meshes to promote the capillary pressure and microchannels underneath to reduce the flow resistance. The analysis indicates that the effective thermal conductivity and the capillary limit of flat heat pipe (FHPs) with this novel micro scale hybrid wicking structure can be significantly enhanced as compared to the reported FHPs. In this paper, the design of this innovative micro scale hybrid wick is illustrated. The fabrication and charging processes are also outlined. The preliminary experimental results show that the effective thermal conductivity can approach 12,270 W/(m·K), which is more than 30 times better than pure copper at approximate 91.3 W input heat.Copyright © 2011 by ASME
The Effective Thermal Conductivities of Composites with 2-D Arrays of Circular and Square Cylinders

A boundary collocation scheme suitable for calculation of the effective thermal conductivity of 2-dimensional periodic arrays is developed. Investigated 2-dimensional arrays include the square arrays of infinitely long circular and square cylinders and hexagonal arrays of infinitely long circular cylinders. The effective thermal conductivity is studied subject to variation in two system parameters: the inclusion volume fraction, f, and the conductivity ratio of the inclusion to the matrix, k 2/k 1 (= σ). The parameter domain investigated is complete, ranging from 0 to the close packing in inclusion volume fractions and from 0 to ∞ in conductivity ratios. The effectiveness of different configurations in improving (if k 2/k 1 > 1) or reducing (if k 2/k 1 < 1) the effective thermal conductivity of the composite is studied with the three arrays. With enhancing (insulating) inclusions, the square array of infinitely long square cylinders is found to be the most efficient configuration in improving (reducing) the effective thermal conductivity of the composite among the three arrays for f below a first crossing volume fraction, f c1 , around 0.56 For f greater than f c1, the square array of infinitely long circular cylinders becomes the most effective configuration. Contour plots of the relative effective thermal conductivity, k eff /k 1, in the f - log (σ) space are obtained, which can be used to infer values of σ from measurement of k eff /k 1 at some given f.
Expression of the FGF‐related proto‐oncogene int‐2 during gastrulation and neurulation in the mouse.

The proto‐oncogene int‐2 has been implicated in the formation of mouse mammary‐tumour‐virus‐induced mammary tumours. Analysis of the predicted coding sequence indicates that int‐2 is a member of the fibroblast growth factor family. Previous studies using Northern blot analysis suggested that normal expression of int‐2 may be confined to extra‐embryonic endoderm lineages of embryonic stages of mouse development. We have used in situ hybridization and Northern blot analysis to examine directly int‐2 expression in embryo stem cells and in the developing embryo from early gastrulation to midsomite stages. Complex patterns of accumulation of int‐2 RNA were observed in embryonic and extra‐embryonic tissues. The data suggest multiple roles for int‐2 in development which may include migration of early mesoderm cells and induction of the otocyst.
The impact of PV orientation in smart grids

In the last years it became a practice photovoltaic power plant to be designed and built with south orientation, the main reason for this being maximum generation of clean energy. This economic approach is justified, from the investors' point of view, but it does not take in to consideration, the different aspects energy produced over the distribution network. Considering the process of decentralization of the energy system that is to a great extend provoked by the systematically conducted policy stimulating the construction of new PV, the problem with the PV modules orientations is very significant and from its correct solution depends the efficient dispatching of the distribution network. The purpose of this article is to explore the possibilities of differently oriented PVs connected to the medium voltage distribution network. The focus is on MV network with differently oriented PV battery systems and different loads. It makes a parallel between the options provided by differently oriented photovoltaic power plants with battery systems for dispatching the network. The article explores the relationship between the orientation of the photovoltaic power plants and their optimal allocation in different nodes. The study proves that for the differently oriented photovoltaic power plants the optimal allocation is not always in the same nodes. It reveals the importance of the orientation of the photovoltaic power plants and not just the estimated power, which is the practice until now, for the proper planning of Distribution Company for newly constructed PV power plants. The research proves that in order to achieve optimal coverage of load profile with minimum investment and electrical losses, the optimum orientation for the construction of photovoltaic power plants with storage systems must take into account not only the orientation of the panels / east, south, west / but also the size of the load and its profile. The investors' interest is also important.