nils-herrmann/clean_scirepeval huggingface dataset:
Long term environmental change in eastern Tasmania: Vegetation, climate and fire at Stoney Lagoon
Year: 2017

Tasmania's dry, inland east is ideally positioned to inform models of late Quaternary environmental change in southern Australasia. Despite this, it remains poorly represented in the palaeoecological record. Here, we seek to address this with a >13,000 year vegetation and fire history from Stoney Lagoon, a site at the eastern margin of Tasmania's inland Midlands plains. Pollen and charcoal analysis indicates that here, a relatively moist early deglacial was followed by a dry later deglacial (ca. 14,000 12,000 cal. BP) when sclerophyll forests became well established and burning increased. This suggests that the Midlands' vegetation responded to the climatic signals characterising Australia's south eastern coast rather than those governing developments in western Tasmania. Dry sclerophyll forest persisted throughout the Holocene; with a pronounced transition from more to less grassy understoreys between ca. 9000 and 7000 cal. BP. From the mid Holocene, the sclerophyll community remains relatively stable. However, increased fire activity and trends in moisture sensitive taxa suggest generally drier conditions coupled with greater hydroclimatic variability under the strengthening influence of the El Nino Southern Oscillation (ENSO) Overall, these results highlight the role of macro scale climatic shifts in shaping vegetation development in Tasmania's inland east, while hinting at the concurrent importance of local ecological drivers. This highlights the need for spatially diverse studies to understand interactions between drivers of long term environmental change in sub humid southern Australia. This research also supports conservation by strengthening understandings of pre colonial baselines in this highly modified landscape.
Chemoprevention of colorectal cancer by black raspberry anthocyanins involved the modulation of gut microbiota and SFRP2 demethylation
Venue: Carcinogenesis
Year: 2018

Freeze dried black raspberry (BRB) powder is considered as a potential cancer chemopreventive agent. In this study, we fed azoxymethane (AOM)/dextran sodium sulfate (DSS) treated C57BL/6J mice with a diet containing BRB anthocyanins for 12 weeks, and this led to a reduction in colon carcinogenesis. These animals had consistently lower tumor multiplicity compared with AOM/DSS treated mice not receiving BRB anthocyanins. In AOM/DSS treated mice, the number of pathogenic bacteria, including Desulfovibrio sp. and Enterococcus spp. was increased significantly, whereas probiotics such as Eubacterium rectale, Faecalibacterium prausnitzii and Lactobacillus were dramatically decreased, but BRB anthocyanins supplement could reverse this imbalance in gut microbiota. BRB anthocyanins also caused the demethylation of the SFRP2 gene promoter, resulting in increased expression of SFRP2, both at the mRNA and protein levels. Furthermore, the expression levels of DNMT31 and DNMT3B, as well as of p STAT3 were downregulated by BRB anthocyanins in these animals. Taken together, these results suggested that BRB anthocyanins could modulate the composition of gut commensal microbiota, and changes in inflammation and the methylation status of the SFRP2 gene may play a central role in the chemoprevention of CRC.
Las TIC en la ensenanza del ingles en educacion basica
Year: 2017

Este trabajo se da a conocer la situacion del sistema educativo de Mexico con respecto a otros paises como Corea del Sur, Paises Bajos, Estados Unidos de America, Finlandia, Canada y Rusia, y la influencia que tienen las TIC en la ensenanza del ingles, su empleo y los beneficios que adquieren profesores y estudiantes del nivel basico. El tipo de estudio realizado es documental descriptivo ya que permite realizar el analisis del uso y manejo de las TIC como estrategias docentes que ayuda a mejorar el rendimiento academico en la produccion escrita del idioma ingles. El trabajo esta enfocado a la ensenanza en ninos de 7 y 8 anos de edad en escuelas privadas. Se demuestra que la materia de ingles es compatible para el uso de las tecnologias ya que hace las clases dinamicas y atractivas para los alumnos, motivando su interes por el aprendizaje de otro idioma.
Realization of density dependent Peierls phases to engineer quantized gauge fields coupled to ultracold matter
Venue: Nature Physics
Year: 2019

Gauge fields that appear in models of high energy and condensed matter physics are dynamical quantum degrees of freedom due to their coupling to matter fields. Since the dynamics of these strongly correlated systems is hard to compute, it was proposed to implement this basic coupling mechanism in quantum simulation platforms with the ultimate goal to emulate lattice gauge theories. Here, we realize the fundamental ingredient for a density dependent gauge field acting on ultracold fermions in an optical lattice by engineering non trivial Peierls phases that depend on the site occupations. We propose and implement a Floquet scheme that relies on breaking time reversal symmetry (TRS) by driving the lattice simultaneously at two frequencies which are resonant with the onsite interactions. This induces density assisted tunnelling processes that are controllable in amplitude and phase. We demonstrate techniques in a Hubbard dimer to quantify the amplitude and to directly measure the Peierls phase with respect to the single particle hopping. The tunnel coupling features two distinct regimes as a function of the modulation amplitudes, which can be characterised by a \mathbb{Z}_2$ invariant. Moreover, we provide a full tomography of the winding structure of the Peierls phase around a Dirac point that appears in the driving parameter space.
Airways remodeling is reversed by aerobic training in an asthma animal model
Year: 2013

Aerobic training (AT) reverses airway remodeling in murine model of asthma; however the effects triggered by AT are poorly known.  Evaluate the effect of AT in airway remodeling and fibrosis mediators in an asthma model.  Balb/c mice were divided in 4 groups (n=8) Control (CT) AT, Ovalbumin (OVA) OVA+AT. OVA groups received 4 i.p. ) 3 and OVA inhalations (1 3% 15 sessions, 30 min. 3xWk) that was maintained during AT. AT (50% max. exercise capacity; 60 min. begun after chronic airway inflammation and it was performed for 4 weeks. After that, tissue lung was collected to evaluated airway smooth muscle (ASM) and epithelium thickness, collagen and elastic fibers contents and mucus expression in the airways evaluated by image analyses. It was also evaluated eosinophil and neutrophil counting and IL 5, OPN, VEGF,TGF b, MMP 9, TIMP 1 by immnunohistochemistry in lung tissues slices.  Sensitized groups presented an increase of eosinophil and neutrophils, airway remodeling features and the expression of IL 5, OPN, VEGF, TGF b, MMP 9 and TIMP 2 *p
CONSENSUS STATEMENT BY THE AMERICAN ASSOCIATION OF CLINICAL ENDOCRINOLOGISTS AND AMERICAN COLLEGE OF ENDOCRINOLOGY ON THE COMPREHENSIVE TYPE 2 DIABETES MANAGEMENT ALGORITHM 2018 EXECUTIVE SUMMARY.
Venue: Endocrine practice official journal of the American College of Endocrinology and the American Association of Clinical Endocrinologists
Year: 2018

ABBREVIATIONS A1C hemoglobin A1C; AACE American Association of Clinical Endocrinologists; ACCORD Action to Control Cardiovascular Risk in Diabetes; ACCORD BP Action to Control Cardiovascular Risk in Diabetes Blood Pressure; ACEI angiotensin converting enzyme inhibitor; ADVANCE Action in Diabetes and Vascular Disease: Preterax and Diamicron MR Controlled Evaluation; AGI alpha glucosidase inhibitor; apo B apolipoprotein B; ASCVD atherosclerotic cardiovascular disease; BAS bile acid sequestrant; BCR QR bromocriptine quick release; BMI body mass index; BP blood pressure; CCB calcium channel blocker; CHD coronary heart disease; CKD chronic kidney disease; CVD cardiovascular disease; DASH Dietary Approaches to Stop Hypertension; DPP4 dipeptidyl peptidase 4; eGFR estimated glomerular filtration rate; ER extended release; FDA Food and Drug Administration; GLP1 glucagon like peptide 1; HDL C high density lipoprotein cholesterol; IMPROVE IT Improved Reduction of Outcomes: Vytorin Efficacy International Trial; LDL C low density lipoprotein cholesterol; LDL P low density lipoprotein particle; Look AHEAD Look Action for Health in Diabetes; NPH neutral protamine Hagedorn; OSA obstructive sleep apnea; RCT randomized controlled trial; SU sulfonylurea; SGLT2 sodium glucose cotransporter 2; SMBG self monitoring of blood glucose; T2D type 2 diabetes; TZD thiazolidinedione; VADT Veterans Affairs Diabetes Trial.
Publicly Available Clinical BERT Embeddings
Venue: ArXiv
Year: 2019

Contextual word embedding models such as ELMo (Peters et al. 2018) and BERT (Devlin et al. 2018) have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been minimally explored on specialty corpora, such as clinical text; moreover, in the clinical domain, no publicly available pre trained BERT models yet exist. In this work, we address this need by exploring and releasing BERT models for clinical text: one for generic clinical text and another for discharge summaries specifically. We demonstrate that using a domain specific model yields performance improvements on three common clinical NLP tasks as compared to nonspecific embeddings. These domain specific models are not as performant on two clinical de identification tasks, and argue that this is a natural consequence of the differences between de identified source text and synthetically non de identified task text.
Spatiotemporal changes in the human lens proteome: Critical insights into long lived proteins
Venue: Progress in Retinal and Eye Research
Year: 2020

The ocular lens is a unique tissue that contains an age gradient of cells and proteins ranging from newly differentiated cells containing newly synthesized proteins to cells and proteins that are as old as the organism. Thus, the ocular lens is an excellent model for studying long lived proteins (LLPs) and the effects of aging and post translational modifications on protein structure and function. Given the architecture of the lens, with young fiber cells in the outer cortex and the oldest cells in the lens nucleus, spatially resolved studies provide information on age specific protein changes. In this review, experimental strategies and proteomic methods that have been used to examine age related and cataract specific changes to the human lens proteome are described. Measured spatio temporal changes in the human lens proteome are summarized and reveal a highly consistent, time dependent set of modifications observed in transparent human lenses. Such measurements have led to the discovery of cataract specific modifications and the realization that many animal systems are unsuitable to study many of these modifications. Mechanisms of protein modifications such as deamidation, racemization, truncation, and protein protein crosslinking are presented and the implications of such mechanisms for other long lived proteins in other tissues are discussed in the context of age related neurological diseases. A comprehensive understanding of LLP modifications will enhance our ability to develop new therapies for the delay, prevention or reversal of age related diseases.
Expressing Objects just like Words: Recurrent Visual Embedding for Image Text Matching
Venue: AAAI
Year: 2020

Existing image text matching approaches typically infer the similarity of an image text pair by capturing and aggregating the affinities between the text and each independent object of the image. However, they ignore the connections between the objects that are semantically related. These objects may collectively determine whether the image corresponds to a text or not. To address this problem, we propose a Dual Path Recurrent Neural Network (DP RNN) which processes images and sentences symmetrically by recurrent neural networks (RNN) In particular, given an input image text pair, our model reorders the image objects based on the positions of their most related words in the text. In the same way as extracting the hidden features from word embeddings, the model leverages RNN to extract high level object features from the reordered object inputs. We validate that the high level object features contain useful joint information of semantically related objects, which benefit the retrieval task. To compute the image text similarity, we incorporate a Multi attention Cross Matching Model into DP RNN. It aggregates the affinity between objects and words with cross modality guided attention and self attention. Our model achieves the state of the art performance on Flickr30K dataset and competitive performance on MS COCO dataset. Extensive experiments demonstrate the effectiveness of our model.
A review on exploration of Fe2O3 photocatalyst towards degradation of dyes and organic contaminants.
Venue: Journal of environmental management
Year: 2020

Photocatalytic degradation is among the promising technology for removal of various dyes and organic contaminants from environment owing to its excellent catalytic activity, low energy utilization, and low cost. As one of potential photocatalysts, Fe2O3 has emerged as an important material for degradation of numerous dyes and organic contaminants caused by its tolerable band gap, wide harvesting of visible light, good stability and recyclability. The present review thoroughly summarized the classification, synthesis route of Fe2O3 with different morphologies, and several modifications of Fe2O3 for improved photocatalytic performance. These include the incorporation with supporting materials, formation of heterojunction with other semiconductor photocatalysts, as well as the fabrication of Z scheme. Explicitly, the other photocatalytic applications of Fe2O3, including for removal of heavy metals, reduction of CO2, evolution of H2, and N2 fixation are also deliberately discussed to further highlight the huge potential of this catalyst. Moreover, the prospects and future challenges are also comprised to expose the unscrutinized criteria of Fe2O3 photocatalyst. This review aims to contribute a knowledge transfer for providing more information on the potential of Fe2O3 photocatalyst. In the meantime, it might give an idea for utilization of this photocatalyst in other environmental remediation application.
Time Aware Transformer based Network for Clinical Notes Series Prediction
Venue: MLHC
Year: 2020

A patient's clinical notes correspond to a sequence of free form text documents generated by healthcare professionals over time. Rich and unique information in clinical notes is useful for clinical decision making. In this work, we propose a time aware transformerbased hierarchical architecture, which we call Flexible Time aware LSTM Transformer (FTL Trans) for classifying a patient's health state based on her series of clinical notes. FTL Trans addresses the problem that current transformer based architectures cannot handle, which is the multi level structure inherent in clinical note series where a note contains a sequence of chucks and a chuck contains further a sequence of words. At the bottom layer, FTL Trans encodes equal length subsequences of a patient's clinical notes "chunks" into content embeddings using a pre trained ClinicalBERT model. Unlike ClinicalBERT, however, FTL Trans merges each content embedding and sequential information into a new position enhanced chunk representation in the second layer by an augmented multi level position embedding. Next, the time aware layer tackles the irregularity in the spacing of notes in the note series by learning a flexible time decay function and utilizing the time decay function to incorporate both the position enhanced chunk embedding and time information into a patient representation. This patient representation is then fed into the top layer for classification. Together, this hierarchical design of FTL Trans successfully captures the multi level sequential structure of the note series. Our extensive experimental evaluation conducted using multiple patient cohorts extracted from the MIMIC dataset illustrates that, while addressing the aforementioned issues, FTL Trans consistently outperforms the state of the art transformer based architectures up to 5% in AUROC and 6% in Accuracy. c (c) 2020 D. Zhang,  Time Aware Transformer based Architecture
Pablo Melogno (compilador) Ciencia, matematica y experiencia. Estudios en historia del conocimiento cientifico, Indice Grupo Editorial, Montevideo, 2015, 184 pp.
Year: 2015

Nada que pueda decirse en unas breves lineas es capaz de capturar la importancia y complejidad de la relacion entre matematica y ciencia; incluso el amplisimo catalogo de intentos por clarificar o simplemente tematizar tal vinculo deja aun un sinnumero de cuestiones abiertas a ulteriores analisis. Ello se debe en buena medida (aunque entre muchos otros factores) a toda una variedad de problemas irresueltos dentro de los campos mismos de las filosofias de la ciencia y de la matematica. Entre ellos se destacan interrogantes acerca del valor cognitivo de las teorias cientificas, la relacion semantica y epistemica entre las leyes cientificas y las regularidades naturales, el estatus ontologico de las entidades matematicas y la fundamentacion y alcance de nuestro conocimiento acerca de ellas. Es claro, sin embargo, que construir un relato del desarrollo de la ciencia y la matematica requiere ineludiblemente de dar cuenta de profundos lazos entre ellas conceptuales, practicos e historicos que se hunden en los origenes mismos del pensamiento.
How the ASNC ImageGuide Registry will guide healthcare policy
Venue: Journal of Nuclear Cardiology
Year: 2013

The American Society of Nuclear Cardiology (ASNC) is the leader in education, advocacy, and quality for the field of nuclear cardiology. ASNC is the voice of more than 4,600 physicians, technologists, and scientists worldwide who are dedicated to the science and practice of nuclear cardiology. Since 1993, ASNC has been establishing the standard for excellence in cardiovascular imaging through the development of clinical guidelines, professional education, and research development. While our organization is centered on the practice of diagnostic imaging, it is important to note that a significant percentage of our membership is invested in the practice of general cardiology as well. ASNC leadership believes strongly that the next opportunity for ASNC to innovate and set the standard of excellence is with the development and implementation of a clinical registry, ImageGuide, to support the many activities and constituencies that comprise our diverse membership. ASNC has been actively engaged in advocating for its members to promote quality, value, and equitable payment and delivery models, and is concerned about the current instability posed by the sustainable growth rate and the way in which it complicates physicians' ability to make desired improvements to their practices, such as the purchase of capital equipment. Data from the American Medical Association  illustrate a divergent trend in practice costs and Medicare payment declining payment makes it difficult to support a practice and staff. ASNC is actively engaged in the promotion of a workable alternative reimbursement model rather than merely searching for a quick or easy solution. Current attempts by Centers for Medicare Medicaid Services (CMS) to reward quality, namely the Physician Quality Reporting System (PQRS) do not provide actionable information to many healthcare professionals, including nuclear cardiology providers. Moreover, PQRS does not contain measures pertinent to nuclear cardiology and other sub specialties. The integration of clinical data registries into new payment models may lead to appropriate and clinically relevant quality improvement metrics, as well as strategies for their use in future quality improvement endeavors. ASNC consistently stresses physicians' and technologists' responsiveness to timely, targeted feedback. Therefore, the development of the ASNC ImageGuide Registry comes at a fortuitous moment.
ISOLASI, IDENTIFIKASI DAN UJI SITOTOKSIK SENYAWA ALKALOID DARI DAUN JOHAR (Senna siamea)
Year: 2016

Telah dilakukan penelitian tentang isolasi alkaloid dari daun Johar (Senna siamea) menggunakan metode ekstraksi dengan pelarut etanol 96% Ekstrak etanol dan serbuk daun Johar diuji penapisan fitokimia. Ekstrak alkaloid dihasilkan dengan cara penggaraman melalui penambahan HCl 2M sampai pH 3 dan diekstraksi dengan etil asetat, lapisan asam yang didapatkan ditambah NH 4 OH hingga pH 9 10 dan diekstraksi dengan etil asetat. Pemisahan alkaloid dengan metode kromatografi lapis tipis preparatif menggunakan fasa diam silika gel GF 254 dan fasa gerak etil asetat:kloroform (8:2) dan uji kemurniannya menggunakan metode KLT dengan berbagai eluen dan KLT dua dimensi. Isolat alkaloid diuji aktivitas sitotoksisitas dengan metode BSLT (Brine Shrimp Lethality Test) penentuan struktur molekul isolat alkaloid dengan metode spektrometri UV Vis, FT IR dan LC MS. Hasil penapisan fitokimia sampel mengandung senyawa flavonoid, tanin, kuinon, saponin, dan alkaloid. Ekstrak alkaloid diperoleh seberat 1,06 gram (0,645% Identifikasi isolat alkaloid menggunakan spektrometri UV Vis menunjukan alkaloid termasuk golongan isokuinolin dengan panjang gelombang 230 nm, 255 nm, dan 335 nm, analisis menggunakan spektrometri FTIR menunjukan isolat alkaloid memiliki gugus fungsi OH, CH 3 C=C, C N, C=O, C O eter. Hasil LC MS diperoleh berat molekul sampel sebesar 214,25 g/mol. Berdasarkan hasil analisis diduga senyawa yang didapatkan adalah senyawa cassiarin A. Hasil uji sitotoksisitas ekstrak alkaloid menunjukkan LC 50 sebesar 18,383 ppm dapat disimpulkan ekstrak alkaloid bersifat sangat sitotoksik.
HUOPM: High Utility Occupancy Pattern Mining
Venue: IEEE Transactions on Cybernetics
Year: 2020

Mining useful patterns from varied types of databases is an important research topic, which has many real life applications. Most studies have considered the frequency as sole interestingness measure to identify high quality patterns. However, each object is different in nature. The relative importance of objects is not equal, in terms of criteria, such as the utility, risk, or interest. Besides, another limitation of frequent patterns is that they generally have a low occupancy, that is, they often represent small sets of items in transactions containing many items and, thus, may not be truly representative of these transactions. To extract high quality patterns in real life applications, this paper extends the occupancy measure to also assess the utility of patterns in transaction databases. We propose an efficient algorithm named high utility occupancy pattern mining (HUOPM) It considers user preferences in terms of frequency, utility, and occupancy. A novel frequency utility tree and two compact data structures, called the utility occupancy list and frequency utility table, are designed to provide global and partial downward closure properties for pruning the search space. The proposed method can efficiently discover the complete set of high quality patterns without candidate generation. Extensive experiments have been conducted on several datasets to evaluate the effectiveness and efficiency of the proposed algorithm. Results show that the derived patterns are intelligible, reasonable, and acceptable, and that HUOPM with its pruning strategies outperforms the state of the art algorithm, in terms of runtime and search space, respectively.