Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Tree-Based Methodological Framework to Infer the Evolutionary History of Mesopolyploid Lineages: An Application to the Brassiceae Tribe (Brassicaceae)

Whole genome duplication events are notably widespread in plants and this poses particular challenges for phylogenetic inference in allopolyploid lineages, i.e. lineages that result from the merging of two or more diverged genomes after interspecific hybridization. The nuclear genomes resulting from allopolyploidization contain homologous gene copies from different evolutionary origins called homoeologs, whose orthologs must be sorted out in order to reconstruct the evolutionary history of polyploid clades. In this study, we propose a methodological approach to resolve the phylogeny of allopolyploid clades focusing on mesopolyploid genomes, which experienced some level of genome reshuffling and gene fractionation across their subgenomes. To illustrate our methodological framework we applied it to a clade belonging to the model Brassicaceae plant family, the Brassiceae tribe, that experienced a mesohexaploidy event. The dataset analysed consists of both publically available genomic sequences and new transcriptomic data according to taxa. The present methodology requires a well-annotated reference genome, for which the identification of the parental subgenome fragments has been performed (e.g. Brassica rapa and Brassica oleracea). Focusing on fully retained genes (i.e. genes for which all homoeologous gene copies inherited from the parental lineages are still present in the reference genome), the method constructs multi-labelled gene trees that allow subsequent assignment of each gene copy to its diploid parental lineage. Once the orthologous copies are identified, genes from the same parental origin are concatenated and tree-building methods are used to reconstruct the species tree. This method allows resolving the phylogenetic relationships (i) among extant species within a mesopolyploid clade, (ii) among the parental lineages of a mesopolyploid lineage, and (iii) between the parental lineages and closely related extant species. We report here the first well-resolved nuclear-based phylogeny of the Brassiceae tribe.
CÓDIGO DE HAMMURABI

(Datos tomados de la publicacion que hizo el doctor Alfonso Reyes, profesor de la Universidad Externado de Colombia, sobre el Codigo y su traduccion al castellano). Si un medico ha tratado un hombre libre con un cuchillo metalico por una herida grave, y lo ha curado, o por un tumor, y ha curado su ojo, recibira diez siclos de plata. Si ha tratado el hijo de un plebeyo, recibira cinco siclos de plata. Si ha tratado un esclavo, el amo de este le entregara dos siclos de plata. Si un medico ha tratado un hombre con un cuchillo metalico por una herida grave, y le ha causado la muerte, o ha abierto un tumor en un hombre con un cuchillo metalico y le ha destruido un ojo, se le amputaran las manos. Si un medico ha tratado el esclavo de un plebeyo con un cuchillo metalico por una herida grave y le ha provocado la muerte, entregara esclavo por esclavo. Si le ha abierto un tumor con un cuchillo metalico y le ha destruido un ojo, pagara la mitad de su precio en plata. Si el medico ha curado un hueso fracturado de un hombre libre o ha restaurado la carne enferma, el paciente entregara al medico cinco siclos de plata. Si fuere el hijo de un plebeyo, se le entregara tres siclos de plata. Si fuere el esclavo de un hombre, el amo del esclavo entregara al medico dos siclos de plata. Si un medico de bueyes o asnos ha tratado un buey o un asno por una herida grave y lo ha curado, el dueno del buey o asno entregara al medico un sexto de un siclo de plata como honorario.
Assisting first generation, low-income students from underserved populations with their transition from high school to a four-year institution

This study examined the lack of guidance and struggles of first-generation, low-income students from underserved populations (FGLISUP). I will use previous research and literature as the groundwork for my research as I explore options that admissions representatives from Eastern Washington University, Central Washington University and Washington State University can use to better serve FGLISUP. This study will use the grounded theory method and the cultural studies theory to better understand this population. This study was conducted using conversational interviews that involved a total of 12 participants, for which six were female and the other six were male. The interviews consisted of six open-ended questions. The participants were encouraged to provide interviewers with as much detail as they wanted to provide regarding their transition and services available to them through the university for guidance during that period of time. The conversational interviews and data were collected for three weeks in accord to fall recruitment scheduling for admissions representatives. The goal of this study was to understand the challenges FGLISUP faced and address them by providing solutions and resources.
Infección por helicobacter pylori en niños e importancia de la placa dental

Helicobacter pylori, bacteria gramnegativa de gran importancia clinico-epidemiologica, debido a su asociacion con enfermedades gastricas como ulcera y adenocarcinoma. Helicobacter pylori es adquirido con mayor frecuencia antes de los 10 anos de edad, predominantemente asintomatico y con aumento progresivo de la seroprevalencia, la cual se ve afectada por factores etnicos, socioeconomicos y malas condiciones de vida. El aislamiento del Helicobacter pylori en saliva y placa dental a creado controversia sobre si la cavidad bucal es un posible reservorio de la bacteria o forma parte de la microflora local. La presente revision destaca la importancia del papel de la placa dental en el diagnostico de Helicobacter pylori en ninos, considerando que la mayoria de los metodos de obtencion de muestras son invasivos, lo que dificulta el diagnostico temprano y el seguimiento de la infeccion, los cuales se ha convertido en puntos claves para combatir el cancer gastrico y las ulceras pepticas en infantes.
Life Cycle Work: A Process Study of the Emergence and Performance of Life Cycle Practice

Life cycle management (LCM) is a concept that goes beyond traditional corporate environmental management, due to its focus on a product’s entire life cycle. The spread of such concepts is usually understood in terms of processes of “diffusion,” whereby ideas spread over time by some inexplicable force. However, diffusion has proven less adequate to describe how ideas spreads in practice. Here, we address this oversight by studying the emergence and performance of what we refer to as life cycle practices. Drawing on an analysis of the development of a sustainability portfolio within a globally operating manufacturing company, we illustrate the kinds of life cycle work involved in dealing with local activities and interests, connecting activities and interests into action nets, performing life cycle practices, and spreading the life cycle idea. Finally, we discuss implications of life cycle work for research in the field of organization and management studies and for LCM research.
Receptive knowledge of intensifying adjectival compounds: Belgian French-speaking CLIL and non-CLIL learners of Dutch and English

ABSTRACT Languages differ in their preferences for particular intensifying constructions. While intensifying adjectival compounds (IACs) (e.g. ijskoud, ice-cold) are productively used to express intensification in Dutch and English, in French this construction is hardly productive. Consequently, French-speaking learners may encounter difficulties acquiring IACs in Dutch/English. As part of a research project on CLIL in French-speaking Belgium, we explore the effect of CLIL on the acquisition of IACs in the target language (TL) Dutch/English through a multiple-choice test. The results confirm that CLIL students (learning English/Dutch) develop greater receptive knowledge of these constructions. Furthermore, the more frequent IACs are more likely to be recognized by the learners. Moreover, even when the CLIL effect is considered alongside other factors, such as the students' extracurricular exposure to the TL and their overall vocabulary, CLIL is still an important predictor of the learners' receptive knowledge of English IACs, in addition to productive and receptive vocabulary. By contrast, current informal contact with the TL and receptive vocabulary are significant predictors of learners' receptive knowledge of Dutch IACs, but CLIL does not significantly contribute to the regression model for the latter language.
Using visual analytics to develop human and machine‐centric models: A review of approaches and proposed information technology

The use of a visual analytical system in machine learning is the basis for the integration of human and the use of his intellectual capabilities in the construction of models. At the same time, visual analytics is used to expand human knowledge and is used as a research tool. We investigate the forms and goals of using visual analytics workflow toward the formation of the final product. Workflow is divided into human‐oriented and machine‐oriented in order to build a model as an information processor and decision‐making mechanism. Models are built on the basis of the end user, which can be either a machine or a human. The concepts of model building and the role of machines and humans in these processes are investigated. A practical implementation of the classification information technology in the studied concept “using opposite model” in the machine‐oriented visual analytics workflow for using the machine model is proposed. The basis for this model is a model formed and used by human. To classify data, human intellectual abilities are used. The boundaries of classes are determined by a human and then projected into a hyperspace of attributes with the formation of a classification model that the machine uses. Information technology allows the machine to use a model built for humans.
In the Fabric of Research: Racial and Gender Stereotypes in Survey Items Assessing Attitudes about Abortion

We investigated the content of survey items to assess whether and how racist and sexist stereotypes are woven into the fabric of research on attitudes about abortion in the United States. We collected and analyzed a comprehensive set of survey items (456 items from 80 studies) used in peer-reviewed research published from 2008 to 2018 in representative and nonrepresentative studies of U.S. respondents. Our analysis was guided by historical narratives that have been influential in shaping representations of women and reproduction in the United States (e.g., the Moynihan Report). With this background, we developed three themes pertaining to how individuals’ attitudes about abortion are measured: we found that items rely on (1) moral, (2) sexual, and (3) financial evaluations of women seeking abortion care. These themes highlighted implicit and explicit judgments of women, including representations of them as unwilling to partner with men and as fiscally and sexually irresponsible. We argue that survey items meant to objectively assess abortion attitudes draw on negative racial and gender stereotypes and that these stereotypes then travel widely under the veneer of scientific objectivity. Critical methods, such as the item bank analysis described in this study, are crucial to discern how inequality, prejudice, and discrimination can be reproduced in the
The gamma-Protocadherins regulate the survival of GABAergic interneurons during developmentally-regulated cell death

Inhibitory interneurons integrate into developing circuits in specific ratios and distributions. In the cortex, the formation of inhibitory networks occurs concurrently with the apoptotic elimination of a third of GABAergic interneurons. The molecular mechanisms that select GABAergic interneurons to survive or die are unknown. Here we report that the clustered Protocadherins regulate GABAergic cell survival in the developing brain. Deletion of the Pcdh-gamma genes (Pcdhgs) from GABAergic neurons in mice causes a severe loss of inhibitory neurons in multiple brain regions and results in motor deficits and seizure activities. By focusing on the neocortex and cerebellar cortex, we demonstrate that GABAergic interneuron loss results from elevated apoptosis during the postnatal wave of Bax-dependent programmed cell death. Pro-survival AKT signals are reduced in Pcdhg-deficient interneurons, diminishing the intrinsic capacity of interneurons to compete and incorporate into developing networks. We propose that the Pcdhgs mediate selective GABAergic interneuron survival to contribute to the formation of balanced inhibitory networks.
Strongholds of Ostrea edulis populations in estuaries in Essex, SE England and their association with traditional oyster aquaculture: evidence to support a MPA designation

Abstract The flat oyster Ostrea edulis has declined significantly in European waters since the 1850s as a result of anthropogenic activity. Ostrea edulis was designated a UK Biodiversity Action Plan Species and Habitat in 1995, and as a Feature of Conservation Importance (FOCI) within the UK Marine & Coastal Access Act 2009. To promote the recovery of oyster beds, a greater understanding of its abundance and distribution is required. Distribution of O. edulis across the proposed Blackwater, Crouch, Roach and Colne MCZ in Essex was determined between 2008 and 2012. Ostrea edulis were present in four estuary zones; with highest sample abundance in the Blackwater and Ray Sand zones. Size structure of populations varied, with the Ray Sand and Colne zones showing a significant lack of individuals with shell height <39 mm. Ostrea edulis occurred in highest number on shell substratum, followed by silty sediments. There were no significant associations between O. edulis abundance or size structure with water column Chl a, suspended solids, oxygen, nitrate or ammonium concentrations, temperature or pH. Highest abundance and most equitable population shell-size distribution for O. edulis were located within, or adjacent to, actively managed aquaculture zones. This suggests that traditional seabed management contributed to the maintenance or recovery of the species of conservation concern. Demonstration that the Essex estuaries were a stronghold for Ostrea edulis in the southern North sea area led to the designation of the Blackwater, Crouch, Roach and Colne estuaries Marine Conservation Zone in 2013.
Clinical Significance of MPL Mutations in Essential Thrombocythemia: Analysis of the PT-1 Cohort.

Activating mutations in MPL, the thrombopoietin receptor, were originally described in idiopathic myelofibrosis (IMF) and subsequently in a small minority of patients with essential thrombocythemia (ET). The prevalence and clinical significance of MPL mutations in ET has not been fully characterised. Using prospectively acquired diagnostic and follow-up data from the large MRC PT-1 study, we describe the clinical characteristics, complications and laboratory features of these mutations. Sequencing the entire MPL cDNA from 19 JAK2 wild-type ET patients did not reveal any mutations outside exon 10. Sequencing MPL exon 10 DNA in 88 ET and 112 IMF patients revealed MPLW515L (n=11), MPLW515K (n=3) and MPLS505N (n=2) mutations. The MPLS505N mutation, previously associated with inherited thrombocythemia, was clearly an acquired mutation in both patients (1 ET and 1 IMF). Sensitive PCR-based methods were then developed for all three mutant MPL alleles and used to genotype 776 patients with ET from the PT-1 trial. MPL mutations were detected in 4% of all patients, comprising 9% of JAK2 wild-type patients. MPL mutant patients were older at diagnosis than both JAK2 wild-type (p=0.0001) and JAK2V617F patients (p=0.09). Compared to JAK2V617F patients, MPL mutant patients had lower hemoglobin and higher platelet levels at diagnosis (p=0.0001 and p=0.006 respectively). There were no differences in diagnostic blood counts between MPL mutant and JAK2 wild-type patients. Diagnostic trephine histology for JAK2V617F (n=168), JAK2 wild-type (n=130) and MPL mutant patients (n=13) was reviewed by three independent histopathologists blinded to mutation status. MPL mutant samples were less cellular than JAK2V617F and JAK2 wild-type samples (p=0.0001 and p=0.003 respectively). Compared to both JAK2V617F and JAK2 wild-type samples, MPL mutant samples had lower erythroid cellularity (p=0.0006 and p=0.005 respectively) and granulocyte cellularity (p=0.006 and p=0.05 respectively). There were no differences in megakaryocyte cellularity or reticulin grade between the three groups. MPL mutant patients had an increased risk of venous thrombosis after trial entry when compared to JAK2 wild-type patients (p=0.02); the rate of venous thrombosis in the MPL mutant group was comparable to the JAK2V617F group. The mutant allele burden (assessed quantitatively by pyrosequencing) was significantly higher in patients with MPLW515K compared to patients with MPLW515L mutations (p=0.0001), suggesting biological differences in the transforming abilities of the two mutations. In colony assays using patient mononuclear cells the MPLW515L mutation was associated with cytokine-independent growth of megakaryocyte colonies but not with erythropoietin-independent erythroid colony growth (4/4 patients). Of 48 MPL mutant patients, only one also carried the JAK2V617F mutation by allele-specific PCR. Taken together, our results describe the prevalence, clinical features and laboratory manifestations of MPL mutations in the context of a large prospective study of ET.
Ipilimumab w leczeniu zaawansowanych czerniaków — komentarz do opisów przypadków

W Polsce ponad 1000 osób rocznie umiera z powodu zaawansowanego czerniaka skóry, mimo że jest to nowotwór łatwy do zdiagnozowania i wyleczenia (głównie za pomocą metod chirurgicznych), o ile zostanie wykryty we wczesnym stadium. W przypadku powstania przerzutów niestety większości chorych nie udaje się wyleczyć. Ostatnie lata przynoszą poprawę tych statystyk. W 2015 roku potwierdzono, że kierunek prowadzonych badań był słuszny i obecnie przeżycia 2-letnie w przerzutowych czerniakach sięgają już 50%. Przełomowe w leczeniu uogólnionych czerniaków są ostatnie 4 lata, co wiąże się z rozwojem zarówno leczenia ukierunkowanego molekularnie, jak i immunoterapii [1]. Nowe terapie wprowadzone do codziennej praktyki klinicznej sprawiły, że obecnie sposób postępowania w przypadku stwierdzenia nieresekcyjnego, przerzutowego czerniaka skóry ma niewiele wspólnego z praktyką kliniczną sprzed 5 lat. W ostatnich 4 latach w Europie zarejestrowano ipilimumab, wemurafenib, dabrafenib, trametynib, niwolumab i pembrolizumab [1–7]. Pierwszą metodą o udowodnionej skuteczności w leczeniu zaawansowanych czerniaków jest immunoterapia nieswoista — w Polsce za pomocą przeciwciała monoklonalnego anty-CTLA4 (anti-cytotoxic T lymphocyte antigen 4) — ipilimumabu w II linii w ramach programu lekowego [2, 3, 5], hamującego ogólnoustrojowe mechanizmy immunosupresji w celu indukcji odpowiedzi przeciwnowotworowej, zarejestrowanego w 2011 roku do leczenia chorych na przerzutowe czerniaki po niepowodzeniu wcześniejszej terapii. W badaniach wykazano znamienne wydłużenie przeżyć całkowitych (OS, overall survival) po zastosowaniu ipilimumabu (Yervoy) przy jednocześnie niewielkim odsetku odpowiedzi. W przeciwieństwie do innych leków odsetek odpowiedzi obiektywnych na leczenie jest jednak niewielki (ok. 10%), ale u około 25% chorych dochodzi do długoletnich przeżyć nieobserwowanych nigdy wcześniej u chorych na zaawansowanego czerniaka. Takie 2 przypadki chorych przedstawiono w niniejszym suplemencie. Wyniki analiz (obejmujących dane ponad 4000 chorych) wskazują, że około 20% pacjentów leczonych tym przeciwciałem żyje nawet 10 lat. Do chwili obecnej terapii ipilimumabem zostało poddanych około 20 000 ludzi na całym świecie. Z uwagi na nietypową kinetykę odpowiedzi na leczenie, która może wystąpić nawet po początkowej progresji, skuteczność leku ocenia się przy wykorzystaniu immunologicznych kryteriów oceny odpowiedzi na leczenie [8]. Z kolei odmienny profil toksyczności ipilimumabu związany z reakcją autoimmunologiczną wymaga znajomości algorytmu postępowania w przypadku wystąpienia powikłań o podłożu immunologicznym. Przeprowadzono 2 badania III fazy z zastosowaniem ipilimumabu u chorych na zaawansowane czerniaki. W badaniu rejestracyjnym MDX010-20 676 chorych, wcześniej leczonych z powodu nieoperacyjnego lub przerzutowego czerniaka, poddano randomizacji w proporcji 3:1:1 do grup: otrzymującej ipilimumab ze szczepionką peptydową gp100, ipilimumab w monote-
Metastatic Prostate and renal cell carcinoma presenting as supra-clavicular lymphadenopathy: Report of two cases

Most metastases of cancers to cervical lymph nodes including supra-clavicular chain are from the head and neck primary tumors. Cancers metastasizing to the supra-calvicular lymph nodes from non-head and neck origin are rare. This occurs most frequently with lung, breast and esophagus. For prostate cancer, the non-regional lymph nodal involvment is very rarely reported. Similarly renal cell carcinoma presents mostly in advanced stage disease with involvment of non-regional lymph nodes is much less common. We present two cases of prostate and renal cell carcinoma who presented with initial manifestation of supraclavicular lymphadenopathy.
Novel target identification using single cell sequencing and electrophysiology of cardiac sympathetic neurons in disease

The activity of cardiac sympathetic nerves from the stellate ganglia is increased in many cardiovascular diseases contributing to the pathophysiology. However, the mechanisms underlying this are unknown. Moreover, clinical studies show their surgical removal is an effective treatment, despite the biophysical properties of these neurons being largely unstudied. We demonstrate that stellate ganglia neurons from prehypertensive spontaneously hypertensive rats are hyperactive and describe in detail their electrophysiological phenotype guided by single cell RNA-sequencing, molecular biology, perforated patch-clamp and computational modelling to uncover the underlying mechanism. The expression of key transcripts is confirmed in human stellate ganglia. We demonstrate the contribution of a plethora of ion channels to stellate ganglia neuronal firing, and show that hyperexcitability is curbed by M-current activators, non-selective sodium current blockers or inhibition of Nav1.1-1.3, Nav1.6 or INaP. These findings have important implications for target discovery to reduce cardiac sympathetic neuron activity pharmacologically without resorting to surgery.
Ulcerative colitis in Albania

Ulcerative colitis is a chronic disease of unknown cause, characterized by ulceration of the colon and rectum mucosa with rectal bleeding and diarrhea. Frequently causes anemia, hypoproteinemia and electrolyte imbalance, and is also less frequently complicated by peritonitis, toxic megacolon or colon carcinoma (Danese and Fiocchi, 2011) review is to ana lyze the most a ffected age and clinical presentations related age groups ; the relationship between age, clinical activity of the disease, hemorrhage and endoscopic findings and to define the correlation between age and disease evolution. This is a retro spective five years study, based on medical cards, which includes 100 patients with ulcerative colitis hospitalized in the University Hospital Center "Mother Theresa", in the Gastroenterology department. Ulcerative colitis is active an average age of 49.7 years. Rectal bleeding correlates with endosc extension of the disease. Pancolitis is mostly found in severe clinical presentations, although it is present in 18-26% in moderate form ulcerative colitis. T he pathology is located in the rectum in 14 severe clinical presentations. Pseudopoly ps are common in every age group, while atrophy and colon cancer are characteric in patients older than There are reciprocal correlations between clinical p endoscopic findings. Age is an important factor affecting clinical activity, endoscopic findings and disease evolution.