nils-herrmann/clean_scirepeval huggingface dataset:
Transcriptome analysis reveals the effects of sugar metabolism and auxin and cytokinin signaling pathways on root growth and development of grafted apple
Venue: BMC Genomics

BackgroundThe root architecture of grafted apple (Malus spp. is affected by various characteristics of the scions. To provide information on the molecular mechanisms underlying this influence, we examined root transcriptomes of M. robusta rootstock grafted with scions of wild type (WT) apple (M. spectabilis) and a more branching (MB) mutant at the branching stage.ResultsThe growth rate of rootstock grafted MB was repressed significantly, especially the primary root length and diameter, and root weight. Biological function categories of differentially expressed genes were significantly enriched in processes associated with hormone signal transduction and intracellular activity, with processes related to the cell cycle especially down regulated. Roots of rootstock grafted with MB scions displayed elevated auxin and cytokinin contents and reduced expression of MrPIN1, MrARF, MrAHP, most MrCRE1 genes, and cell growth related genes MrGH3, MrSAUR and MrTCH4. Although auxin accumulation and transcription of MrPIN3, MrALF1 and MrALF4 tended to induce lateral root formation in MB grafted rootstock, the number of lateral roots was not significantly changed. Sucrose, fructose and glucose contents were not decreased in MB grafted roots compared with those bearing WT scions, but glycolysis and tricarboxylic acid cycle metabolic activities were repressed. Root resistance and nitrogen metabolism were reduced in MB grafted roots as well.ConclusionsOur findings suggest that root growth and development of rootstock are mainly influenced by sugar metabolism and auxin and cytokinin signaling pathways. This study provides a basis that the characteristics of scions are related to root growth and development, resistance and activity of rootstocks.
Protein breakdown in cancer cachexia.
Venue: Seminars in cell developmental biology

Skeletal muscle is a highly adaptive tissue, capable of altering muscle fiber size, functional capacity and metabolism in response to physiological stimuli. However, pathological conditions such as cancer growth compromise the mechanisms that regulate muscle homeostasis, resulting in loss of muscle mass, functional impairment and compromised metabolism. This tumor induced condition is characterized by enhanced muscle protein breakdown and amino acids release that sustain liver gluconeogenesis and tissue protein synthesis. Proteolysis is controlled by the two most important cellular degradation systems, the ubiquitin proteasome and autophagy lysosome. These systems are carefully regulated by different signalling pathways that determine protein and organelle turnover. In this review we will describe the involvement of the ubiquitin proteasome and autophagy lysosome systems in cancer cachexia and the principal signalling pathways that regulate tumor induced protein breakdown in muscle.
Cancer Cachexia: Beyond Weight Loss.
Venue: Journal of oncology practice

Cancer cachexia is a multifactorial syndrome characterized by skeletal muscle loss leading to progressive functional impairment. Despite the ubiquity of cachexia in clinical practice, prevention, early identification, and intervention remain challenging. The impact of cancer cachexia on quality of life, treatment related toxicity, physical function, and mortality are well established; however, establishing a clinically meaningful definition has proven challenging because of the focus on weight loss alone. Attempts to more comprehensively define cachexia through body composition, physical functioning, and molecular biomarkers, while promising, are yet to be routinely incorporated into clinical practice. Pharmacologic agents that have not been approved by the US Food and Drug Administration but that are currently used in cancer cachexia (ie, megestrol, dronabinol) may improve weight but not outcomes of interest such as muscle mass, physical activity, or mortality. Their routine use is limited by adverse effects. For the practicing oncologist, early identification and management of cachexia is critical. Oncologists must recognize cachexia beyond weight loss alone, focusing instead on body composition and physical functioning. In fact, becoming emaciated is a late sign of cachexia that characterizes its refractory stage. Given that cachexia is a multifactorial syndrome, it requires early identification and polymodal intervention, including optimal cancer therapy, symptom management, nutrition, exercise, and psychosocial support. Consequently, oncologists have a role in ensuring that these resources are available to their patients. In addition, in light of the promising investigational agents, it remains imperative to refer patients with cachexia to clinical trials so that available options can be expanded to effectively treat this pervasive problem.
Understanding cachexia as a cancer metabolism syndrome
Venue: Oncogenesis

Metabolic reprogramming occurs in tumors to foster cancer cell proliferation, survival and metastasis, but as well at a systemic level affecting the whole organism, eventually leading to cancer cachexia. Indeed, as cancer cells rely on external sources of nitrogen and carbon skeleton to grow, systemic metabolic deregulation promoting tissue wasting and metabolites mobilization ultimately supports tumor growth. Cachectic patients experience a wide range of symptoms affecting several organ functions such as muscle, liver, brain, immune system and heart, collectively decreasing patients' quality of life and worsening their prognosis. Moreover, cachexia is estimated to be the direct cause of at least 20% of cancer deaths. The main aspect of cachexia syndrome is the unstoppable skeletal muscle and fat storage wasting, even with an adequate caloric intake, resulting in nutrient mobilization both directly as lipid and amino acids and indirectly as glucose derived from the exploitation of liver gluconeogenesis that reaches the tumor through the bloodstream. From a metabolic standpoint, cachectic host develops a wide range of dysfunctions, from increased insulin and IGF 1 resistance to induction of mitochondrial uncoupling proteins and fat tissue browning resulting in an increased energy expenditure and heat generation, even at rest. For a long time, cachexia has been merely considered an epiphenomenon of end stage tumors. However, in specific tumor types, such as pancreatic cancers, it is now clear that patients present markers of tissue wasting at a stage in which tumor is not yet clinically detectable, and that host amino acid supply is required for tumor growth. Indeed, tumor cells actively promote tissue wasting by secreting specific factors such as parathyroid hormone related protein and micro RNAs. Understanding the molecular and metabolic mediators of cachexia will not only advance therapeutic approaches against cancer, but also improve patients' quality of life.
Cachexia in patients with oesophageal cancer
Venue: Nature Reviews Clinical Oncology

Oesophageal cancer is a debilitating disease with a poor prognosis, and weight loss owing to malnutrition prevails in the majority of patients. Cachexia, a multifactorial syndrome characterized by the loss of fat and skeletal muscle mass and systemic inflammation arising from complex host tumour interactions is a major contributor to malnutrition, which is a determinant of tolerance to treatment and survival. In patients with oesophageal cancer, cachexia is further compounded by eating difficulties owing to the stage and location of the tumour, and the effects of neoadjuvant therapy. Treatment with curative intent involves exceptionally extensive and invasive surgery, and the subsequent anatomical changes often lead to eating difficulties and severe postoperative malnutrition. Thus, screening for cachexia by means of percentage weight loss and BMI during the cancer trajectory and survivorship periods is imperative. Additionally, markers of inflammation (such as C reactive protein) dysphagia and appetite loss should be assessed at diagnosis. Routine assessments of body composition are also necessary in patients with oesophageal cancer to enable assessment of skeletal muscle loss, which might be masked by sarcopenic obesity in these patients. A need exists for clinical trials examining the effectiveness of therapeutic and physical activity based interventions in mitigating muscle loss and counteracting cachexia in these patients.
Lipolytic and thermogenic depletion of adipose tissue in cancer cachexia.
Venue: Seminars in cell developmental biology

Although muscle wasting is the obvious manifestation of cancer cachexia that impacts on patient quality of life, the loss of lipid reserves and metabolic imbalance in adipose tissue also contribute to the devastating impact of cachexia. Depletion of fat depots in cancer patients is more pronounced than loss of muscle and often precedes, or even occurs in the absence of, reduced lean body mass. Rapid mobilisation of triglycerides stored within adipocytes to supply the body with fatty acids in periods of high energy demand is normally mediated through a well defined process of lipolysis involving the lipases ATGL, HSL and MGL. Studies into how these lipases contribute to fat loss in cancer cachexia have revealed the prominent role for ATGL in initiating lipolysis during adipose tissue atrophy, together with links between tumour derived factors and the signalling pathways that control lipid flux within fat cells. The recent findings of increased thermogenesis in brown fat during cancer cachexia indicate that metabolically active adipose tissue contributes to the imbalance in energy homeostasis involved in catabolic wasting. Such energetically futile use of fatty acids liberated from adipose tissue to generate heat represents a maladaptive response in conjunction with anorexia experienced by cancer patients. As IL 6 release by tumours provokes lipolysis and activates the thermogenic programme in brown fat, this review explores the overlap in dysregulated metabolic processes due to inflammatory mediators in cancer cachexia and other disease states characterised by elevated cytokines such as obesity and diabetes.
Hysteroscopy in recurrent in vitro fertilisation failure (TROPHY) a multicentre, randomised controlled trial
Venue: The Lancet

The success rate of in vitro fertilisation (IVF) remains low and many women undergo multiple treatment cycles. A previous meta analysis suggested hysteroscopy could improve outcomes in women who have had recurrent implantation failure; however, studies were of poor quality and a definitive randomised trial was needed. In the TROPHY trial we aimed to assess whether hysteroscopy improves the livebirth rate following IVF treatment in women with recurrent failure of implantation.  We did a multicentre, randomised controlled trial in eight hospitals in the UK, Belgium, Italy, and the Czech Republic. We recruited women younger than 38 years who had normal ultrasound of the uterine cavity and history of two to four unsuccessful IVF cycles. We used an independent web based trial management system to randomly assign (1:1) women to receive outpatient hysteroscopy (hysteroscopy group) or no hysteroscopy (control group) in the month before starting a treatment cycle of IVF (with or without intracytoplasmic sperm injection) A computer based algorithm minimised for key prognostic variables: age, body mass index, basal follicle stimulating hormone concentration, and the number of previous failed IVF cycles. The order of group assignment was masked to the researchers at the time of recruitment and randomisation. Embryologists involved in the embryo transfer were masked to group allocation, but physicians doing the procedure knew of group assignment and had hysteroscopy findings accessible. Participants were not masked to their group assignment. The primary outcome was the livebirth rate (proportion of women who had a live baby beyond 24 weeks of gestation) in the intention to treat population.   Between Jan 1, 2010, and Dec 31, 2013, we randomly assigned 350 women to the hysteroscopy group and 352 women to the control group. 102 (29% of women in the hysteroscopy group had a livebirth after IVF compared with 102 (29% women in the control group (risk ratio 1*0, 95% CI 0*79 1*25; p=0*96) No hysteroscopy related adverse events were reported.  Outpatient hysteroscopy before IVF in women with a normal ultrasound of the uterine cavity and a history of unsuccessful IVF treatment cycles does not improve the livebirth rate. Further research into the effectiveness of surgical correction of specific uterine cavity abnormalities before IVF is warranted.
Maximum efficiency point tracking for resonant wireless power transfer

The use of wireless technologies to power devices has many practical benefits however it is commonly disregarded due to losses in transferring power in this way. The most common method for wireless power transfer is via Strongly Coupled Magnetic Resonances (SCMR) which transfers energy by using the mutual inductance between coils. Generally, to achieve a high efficiency wireless power transfer the transmitter frequency must match the self resonant frequency of its power receiver. However, techniques in literature that continuously measure the self resonant frequency of a working LC resonant circuit (i.e. the power receiver) have limitations. In this paper, a phase shift control based Maximum Efficiency Point Tracking (MEPT) hypothesis is proposed and examined. Finally, a prototype wireless power system that utilises this methodology is built to demonstrate that it can be used to successfully control a wireless power transfer system at its optimum frequency and hence achieve maximum efficiency.
Methods In Cell Biology

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Spatiotemporal data as the foundation of an archaeological stratigraphy extraction and management system

Transforming relations between stratigraphic units of an archaeological excavation to a formal model like the Harris Matrix is a challenging task. Especially when the number of stratigraphic units is large or when spatiotemporal relations are complex, such models are difficult to generate. This paper describes a novel procedure for the automated construction of Harris Matrices involving the use of open source database software programs and tools. The procedure is based on an algorithm for the detection of spatial relations between stratigraphic units. For each stratigraphic unit (represented by commonly available 2D polygons) all possible top down spatial relations are defined. These large series of relations are then iteratively validated, retaining a limited number of topological coherent sequences. These relations are required for the definition of stratigraphic sequences. To facilitate the presentation of resulting sequences, a stratigraphic diagram is incorporated into a graphical user interface on top of a geodatabase management system and web feature service (WFS) This interface is supplemented with attributes of each stratigraphic unit and with a virtual representation in an embedded 2D map viewer and 3D viewer. The link between sequences and cartographic representations of stratigraphic units by the underlying system enables interactions between various elements of the dataset while taking into account 2D and 3D spatial information, stratigraphic relations and attribute displays. Three theoretical datasets are used to develop and test the workflow. Furthermore, a reference dataset is used to validate this workflow. We find that expert knowledge remains indispensable for the interpretation and validation of both data sources and results. Nevertheless, the robustness of the results of this study illustrate the potential of the proposed procedure for use in automated Harris Matrix construction based on sequences of stratigraphic unit polygons. In employing this procedure, systems may facilitate the management of archaeological (spatiotemporal) data in cost and time efficient research infrastructures.
Pedagogical Reasoning in Teacher Education

The foundations on which teaching is constructed hint at ways of thinking and knowing that shape pedagogy and illustrate why simplistic notions of teaching as telling and learning as listening do not suffice (Loughran, Curric Inq 43(1):118 141, 2013) As a consequence, teaching is perhaps best understood as being problematic because it exists in what Schon (The reflective practitioner: how professionals think in action.Basic Books, New York, 1983) described as the swampy lowlands where important but messy problems exist that cannot be simply resolved or technically managed. Teachers work with uncertainty in an 'indeterminate zone of practice' (Schon DA, Educating the reflective practitioner. Jossey Bass, San Francisco, 1987) in which professional knowledge develops in response to, and is informed by, the context. In exploring the uncertainty inherent in navigating the swampy lowlands of practice, pedagogical reasoning the scaffolding that supports the sophisticated business of professional practice comes into sharp focus. Understanding pedagogical reasoning, how it develops and the manner in which it influences practice is important. Making that clear for others, especially students of teaching, is a challenge that should not be eschewed in teacher education programmes.
Banks' Specialization versus Diversification in the Loan Portfolio

Do banks with a specialized credit portfolio have superior selection and monitoring abilities? Controlling for the composition of the banks' loan portfolios, we show that specialized banks have lower loan loss rates. We also see that for more focused German banks in our sample period 2003 2011 the standard deviation of loan loss rates seems to be lower. Moreover, the loan loss rate of a given industry in a bank's loan portfolio is lower if the bank has a major exposure to that industry.
Language choices and symbolic power in intercultural communication: A case study of a multilingual, immigrant Filipino woman in South Korea

This paper is a case study of a Filipino woman who migrated to Korea to marry a Korean farmer and who ends up using her knowledge of English to navigate power differences in her exchanges with Korean interlocutors. I extend the tradition of research on intercultural communication by drawing on Bourdieu's concept of symbolic power. Employing the ethnography of an embedded case study, this paper adopts inductive thematic analysis and discourse analysis to show (a) Natalie's attitudes toward Korean and English, (b) her use of English in the Korean school setting as a parent to destabilize power differences, (c) her encounters with institutional/ideological walls that reinforce power differences, and (d) her daughter's strategies of appropriating her mother's English speaking status. The data reveal how Natalie being in an inferior social position due to her status as a foreign bride strategically used the symbolic power of English in an effort to position herself as a legitimate interlocutor. The clash between the global legitimacy of English and the local legitimacy of Korean replicates on a microscale the larger symbolic struggles that are going on the geopolitical level in intercultural encounters. By discussing the historical, (post)colonial reality that study participants faced, this paper ultimately demonstrates a conflict between various symbolic orders and highlights the eminently paradoxical struggle for symbolic power.
PATHWAYS INTO STEM AMONG LOW INCOME, URBAN IMMIGRANT EMERGENT BILINGUAL/MULTILINGUAL YOUNG ADULTS: OPPORTUNITY, ACCESS, AND PERSISTENCE

Pathways into STEM Among Urban, Low Income Immigrant Emergent Bilingual/Multilingual  This project builds upon the author's multi year critical ethnographic study of urban immigrant students and their trajectories into STEM (science, technology, engineering, or mathematics) from high school through their transition to college. At its core, this study investigates the paths of over three dozen newcomer immigrant English language learner students in high poverty urban neighborhoods who are not generally considered "legitimate contenders" for Bachelor's degrees in STEM fields on the basis of such characteristics as test scores, high school and prior preparation, and age. The students are followed through their high school experiences, their transition to college, and through their current progress in college, with explicit attention paid to key mediating experiences and relationships in and especially outside of the classroom that were associated with their toward persistence and success. Thick description and analysis of the students and their experiences, among those who persisted as well as the minority who switched out of STEM majors, helps to demonstrate a proof of concept of these students' ability to succeed while painting a comprehensive picture of their march forward to degrees in STEM fields against a backdrop of economic, linguistic, and other barriers to entry and success. Using a framework of social and capital and resilience theories, this work has uncovered a number of themes and factors that will help educators to better understand the evolution of these traditionally marginalized students' STEM related interests, skills, and career plans. The findings center around students' exposure to research internships and other STEM enrichment