Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanical property assessment for establishing design values of western juniper

Western juniper (Juniperus occidentalis) is a conifer that is native to Oregon, California, Washington, Nevada, and Idaho. Juniper is highly decay resistant and, therefore, is a popular choice for fence posts and landscape timbers. Forest management practices over the past 100 yr have resulted in an immense population increase in western juniper stands, transforming the grasslands/sagebrush biome into juniper forests. Landowners have been encouraged to cut back western juniper to restore grassland habitat, but there is no major market associated with juniper lumber. This study assessed the mechanical properties of western juniper to develop its design values for inclusion in the National Design Specification. Small clear samples were prepared from juniper harvested from three locations in eastern Oregon, one location in northeast California, and one location in southwest Idaho according to ASTM D143 for compression, bending, and shear. Average strength values were calculated and compared with similar wood species. Most properties were similar to those of other species, but modulus of elasticity was significantly lower. Compressive properties of western juniper also differed, with compression parallel-to-grain being lower and compression perpendicular-to-grain being relatively higher. Differences between species might be attributed to cell wall structure and distribution of lignin in the cells. Design values for western juniper were calculated using the strength values to establish allowable properties for visually graded lumber. © 2018 by the Society of Wood Science and Technology.
In Search of an Alternative to Shareholder Value Maximization

This paper argues that mainstream economic theory, far from providing an indisputable plea in favor of shareholder value-maximization, offers striking arguments showing quite the opposite : profit-maximization cannot be a legitimate goal for private firms. This opens the door for a widening of a company's goal. We argue that it should include the concern of all the stakeholders of a company, and cannot be adequately addressed uniquely by Pigouvian taxes or by property rights. Coming to terms with this broad understanding of a company's goal should imply the internalization of the stakeholders' concern within the legal structure of the firm -- as in the case of the SCIC in France or the CIC in the UK.
Oncoplastic surgery for the conservative treatment of breast cancer in Perú’s National Cancer Institute

Background Oncoplastic surgery for breast cancer (OPS) has been a surgical trend for the past 25 years. In 2012, OPS has been introduced as the standard treatment for a selected group of patients at the National Cancer Institute of Peru (INEN). The aim of this study is to describe our findings. Methods This is a retrospective and descriptive study that identified demographics, tumour-pathologic features and includes patients solely treated since diagnosis until late follow-up at INEN. These OPS patients were identified from the conservative treatment patients group by review of medical charts and creation of a database for periods December 2005 through December 2015. Results A total of 146 patients were ruled in by the inclusion criteria. All patients were Peruvian females, 56.2% being 51 or older. 93.8% had core biopsy diagnosis of breast cancer and 52.1% located at the upper outer quadrant. 79.5% patients had upfront OPS and the round block (43.2%) and reduction/mastopexy (23.3%) were the most used techniques. pT2 was the most frequent size (54.7%). We achieved negative margins in 134 patients (93.2%) in a single procedure. Of 29 patients, who had neoadjuvant treatment, 11 achieved pCR. Only 5.5% had pN2 or higher. 95.2% received complimentary external beam radiotherapy. Conclusions OPS has proven to be a reliable surgical option, both for aesthetic and oncologic outcomes. Important points for achieving these results are breast surgeons having properly trained under the OPS philosophy and knowing the patients’ characteristics for correct technique selection.
Fatty acid composition of plasma phospholipids and risk of prostate cancer in a case-control analysis nested within the European Prospective Investigation into Cancer and Nutrition 1 – 3

Background: Plausible biological mechanisms underlie possible associations between fatty acids in blood and risk of prostate cancer; epidemiologic evidence for an association, however, is inconsistent. Objective: The objectives were to assess the association between plasma phospholipid fatty acids and risk of total prostate cancer by stage and grade. Design: This was a nested case-control analysis of 962 men with a diagnosis of prostate cancer after a median follow-up time of 4.2 y and 1061 matched controls who were taking part in the European Prospective Investigation into Cancer and Nutrition. The fatty acid composition of plasma phospholipids was measured by gas chromatography, and the risk of prostate cancer was estimated by using conditional logistic regression with adjustment for lifestyle variables. Results: We found a positive association between palmitic acid and risk of total, localized, and low-grade prostate cancer. The risk of prostate cancer for men in the highest quintile compared with the lowest quintile of palmitic acid was 1.47 (95% CI: 0.97, 2.23; P for trend 0.032). We found an inverse association between stearic acid and the risk of total, localized, and low-grade prostate cancer; men in the highest quintile of stearic acid had a relative risk of 0.77 (95% CI: 0.56, 1.06; P for trend 0.03). There were significant positive associations between myristic, -linolenic, and eicosapentaenoic acids and risk of high-grade prostate cancer. Conclusion: The associations between palmitic, stearic, myristic, -linolenic, and eicosapentaenoic acids and prostate cancer risk may reflect differences in intake or metabolism of these fatty acids between the precancer cases and controls and should be explored further. Am J Clin Nutr 2008;88:1353–63.
Im2Struct: Recovering 3D Shape Structure from a Single RGB Image

We propose to recover 3D shape structures from single RGB images, where structure refers to shape parts represented by cuboids and part relations encompassing connectivity and symmetry. Given a single 2D image with an object depicted, our goal is automatically recover a cuboid structure of the object parts as well as their mutual relations. We develop a convolutional-recursive auto-encoder comprised of structure parsing of a 2D image followed by structure recovering of a cuboid hierarchy. The encoder is achieved by a multi-scale convolutional network trained with the task of shape contour estimation, thereby learning to discern object structures in various forms and scales. The decoder fuses the features of the structure parsing network and the original image, and recursively decodes a hierarchy of cuboids. Since the decoder network is learned to recover part relations including connectivity and symmetry explicitly, the plausibility and generality of part structure recovery can be ensured. The two networks are jointly trained using the training data of contour-mask and cuboid-structure pairs. Such pairs are generated by rendering stock 3D CAD models coming with part segmentation. Our method achieves unprecedentedly faithful and detailed recovery of diverse 3D part structures from single-view 2D images. We demonstrate two applications of our method including structure-guided completion of 3D volumes reconstructed from single-view images and structure-aware interactive editing of 2D images.
Noble gas ion beams in materials science for future applications and devices

Helium ion microscopy (HIM), enabled by a gas field ion source (GFIS), is an emerging imaging and nanofabrication technique compatible with many applications in materials science. The scanning electron microscope (SEM) has become ubiquitous in materials science for high-resolution imaging of materials. However, due to the fundamental limitation in focusing of electron beams, ion-beam microscopy is now being developed (e.g., at 20 kV the SEM beam diameter ranges from 0.5 to 1 nm, whereas the HIM offers 0.35 nm). The key technological advantage of the HIM is in its multipurpose design that excels in a variety of disciplines. The HIM offers higher resolution than the best available SEMs as well as the traditional gallium liquid-metal ion source (LMISs) focused ion beams (FIBs), and is capable of imaging untreated biological or other insulating samples with unprecedented resolution, depth of field, materials contrast, and image quality. GFIS FIBs also offer a direct path to defect engineering via ion implantation, three-dimensional direct write using gaseous and liquid precursors, and chemical-imaging options with secondary ion mass spectrometry. HIM covers a wide range of tasks that otherwise would require multiple tools or specialized sample preparation. In this article, we describe the underlying technology, present materials, relevant applications, and offer an outlook for the potential of FIB technology in processing materials.
Grounding natural language with autonomous interaction

The resurgence of deep neural networks has resulted in impressive advances in natural language processing (NLP). This success, however, is contingent on access to large amounts of structured supervision, often manually constructed and unavailable for many applications and domains. In this thesis, I present novel computational models that integrate reinforcement learning with language understanding to induce grounded representations of semantics. Using unstructured feedback, these techniques not only enable task-optimized representations which reduce dependence on high quality annotations, but also exploit language in adapting control policies across different environments. First, I describe an approach for learning to play text-based games, where all interaction is through natural language and the only source of feedback is in-game rewards. Employing a deep reinforcement learning framework to jointly learn state representations and action policies, our model outperforms several baselines on different domains, demonstrating the importance of learning expressive representations. Second, I exhibit a framework for utilizing textual descriptions to tackle the challenging problem of cross-domain policy transfer for reinforcement learning (RL). We employ a model-based RL approach consisting of a differentiable planning module, a model-free component and a factorized state representation to effectively make use of text. Our model outperforms prior work on both transfer and multi-task scenarios in a variety of different environments. Finally, I demonstrate how reinforcement learning can enhance traditional NLP systems in low resource scenarios. In particular, I describe an autonomous agent that can learn to acquire and integrate external information to enhance information extraction. Our experiments on two databases – shooting incidents and food adulteration cases – demonstrate that our system significantly improves over traditional extractors and a competitive meta-classifier baseline. Thesis Supervisor: Regina Barzilay Title: Professor of Electrical Engineering and Computer Science
Design of a wearable physical activity monitoring system using mobile phones and accelerometers

This paper describes the motivation for, and overarching design of, an open-source hardware and software system to enable population-scale, longitudinal measurement of physical activity and sedentary behavior using common mobile phones. The “Wockets” data collection system permits researchers to collect raw motion data from participants who wear multiple small, comfortable sensors for 24 hours per day, including during sleep, and monitor data collection remotely.
iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components

Meiosis and recombination are the two opposite aspects that coexist in a DNA system. As a driving force for evolution by generating natural genetic variations, meiotic recombination plays a very important role in the formation of eggs and sperm. Interestingly, the recombination does not occur randomly across a genome, but with higher probability in some genomic regions called “hotspots”, while with lower probability in so-called “coldspots”. With the ever-increasing amount of genome sequence data in the postgenomic era, computational methods for effectively identifying the hotspots and coldspots have become urgent as they can timely provide us with useful insights into the mechanism of meiotic recombination and the process of genome evolution as well. To meet the need, we developed a new predictor called “iRSpot-TNCPseAAC”, in which a DNA sample was formulated by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample according to its genetic codes. The former was used to incorporate its local or short-rage sequence order information; while the latter, its global and long-range one. Compared with the best existing predictor in this area, iRSpot-TNCPseAAC achieved higher rates in accuracy, Mathew’s correlation coefficient, and sensitivity, indicating that the new predictor may become a useful tool for identifying the recombination hotspots and coldspots, or, at least, become a complementary tool to the existing methods. It has not escaped our notice that the aforementioned novel approach to incorporate the DNA sequence order information into a discrete model may also be used for many other genome analysis problems. The web-server for iRSpot-TNCPseAAC is available at http://www.jci-bioinfo.cn/iRSpot-TNCPseAAC. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to obtain their desired result without the need to follow the complicated mathematical equations.
Identifying which conduits are moving water in woody plants: a new HRCT-based method

In vivo imaging methods are useful for examination of plant vascular tissues, particularly in the identification of fluid vs gas-filled conduits; however, these methods may not allow for the simple identification of conductive conduits. Our aim in the present study was to develop a method that would allow for the in vivo identification of conductive conduits. Intact plants and segments of grapevine (Vitis vinifera L.) and intact American chestnut (Castanea dentata (Marshall) Borkh. ) saplings were examined. We found that iohexol, a water soluble iodine-rich molecule, was a useful contrast agent. We also stained the xylem of segments and gas- dried samples to compare between intact scans and excised segments. Iohexol could be readily fed through cut roots or stems into the transpiration stream, was successfully transported through the xylem and marked conductive vessels within high-resolution computed tomography (HRCT) scans. Iohexol results were comparable to those obtained by staining cut segments, with iohexol detecting greater numbers of smaller conduits in some samples. Samples contained gas-filled conduits, as well as both conductive (containing iohexol tracer) and non-conductive (no iohexol tracer) fluid-filled vessels. Fluid-filled non-conductive vessels were likely still developing or were not connected to the sap stream by a low resistance pathway. We found minimal differences between intact and excised segments other than excision-related dilution of iohexol. Both vessels and vasicentric tracheids were filled with iohexol in chestnut, providing a new tool to study the functions of these different cell types. The use of iohexol as a tracer to identify conductive vessels may greatly improve the utility of HRCT as a tool in the study of plant hydraulic function. Future studies using HRCT will likely need to incorporate conductive vessel markers or controls into experiments due to the presence of non-conductive fluid-filled vessels within the xylem.
Update on the Treatment of Diabetic Retinopathy

Retinopathy is the most feared complication of diabetes, compromising quality of life in most sufferers. Almost all patients with type 1 diabetes will develop retinopathy over a 15- to 20-year period, and approximately 20–30% will advance to the blinding stage of the disease[1]. Greater than 60% of patients with type 2 diabetes will have retinopathy. This situation is highlighted by the frightening statistic that diabetic retinopathy (DR) remains the most common cause of vision impairment in people of working age in Western society. With the global epidemic of type 2 diabetes, this predicament is set to worsen as over 360 million people are projected to suffer from diabetes and its complications by 2030. Vision loss from diabetes is due to a number of factors, including haemorrhage from new and poorly formed blood vessels, retinal detachment due to contraction of deposited fibrous tissue, and neovascular glaucoma resulting in an increase in intraocular pressure. Diabetic macular oedema is now the principal cause of vision loss in diabetes and involves leakage from a disrupted blood-retinal barrier. In terms of treatment, there is clear evidence that strict metabolic and blood pressure control can lower the risk of developing DR and reduce disease progression. Laser photocoagulation and vitrectomy are effective in preventing severe vision loss in DR, particularly in the most advanced stages of the disease. However, both procedures have limitations. This review examines evidence from preclinical and clinical studies that shows that targeting inhibition of the renin-angiotensin system, vascular endothelial growth factor, corticosteroids, protein kinase C, growth hormone, and advanced glycation end-products are potential treatments for DR.
Iron bioavailability and dietary reference values 1 – 4

Iron differs from other minerals because iron balance in the human body is regulated by absorption only because there is no physiologic mechanism for excretion. On the basis of intake data and isotope studies, iron bioavailability has been estimated to be in the range of 14–18% for mixed diets and 5–12% for vegetarian diets in subjects with no iron stores, and these values have been used to generate dietary reference values for all population groups. Dietary factors that influence iron absorption, such as phytate, polyphenols, calcium, ascorbic acid, and muscle tissue, have been shown repeatedly to influence iron absorption in single-meal isotope studies, whereas in multimeal studies with a varied diet and multiple inhibitors and enhancers, the effect of single components has been, as expected, more modest. The importance of fortification iron and food additives such as erythorbic acid on iron bioavailability from a mixed diet needs clarification. The influence of vitamin A, carotenoids, and nondigestible carbohydrates on iron absorption and the nature of the “meat factor” remain unresolved. The iron status of the individual and other host factors, such as obesity, play a key role in iron bioavailability, and iron status generally has a greater effect than diet composition. It would therefore be timely to develop a range of iron bioavailability factors based not only on diet composition but also on subject characteristics, such as iron status and prevalence of obesity. Am J Clin Nutr 2010;91(suppl):1461S–7S.
Frequent cross-resistance to rilpivirine among subtype C HIV-1 from first-line antiretroviral therapy failures in South Africa

Background Rilpivirine (TMC278LA) is a promising drug for pre-exposure prophylaxis of HIV-1 because of its sub-nanomolar potency and long-acting formulation; however, increasing transmission of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 with potential cross-resistance to rilpivirine could reduce its preventive efficacy. This study investigated rilpivirine cross-resistance among recombinant subtype C HIV-1 derived from 100 individuals failing on first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy in South Africa whose samples were sent for routine HIV-1 drug resistance testing to Lancet Laboratories (Johannesburg, South Africa). Methods Plasma samples were selected from individuals with HIV-1 RNA > 10,000 copies/ml and ≥1 non-nucleoside reverse transcriptase inhibitor-resistance mutation in reverse transcriptase. Recombinant HIV-1LAI-containing bulk-cloned full-length reverse transcriptase sequences from plasma were assayed for susceptibility to nevirapine (NVP), efavirenz (EFV) and rilpivirine in TZM-bl cells. Fold-change (FC) decreases in drug susceptibility were calculated against a mean IC50 from 12 subtype C HIV-1 samples from treatment-naïve individuals in South Africa. Cross-resistance was evaluated based on biological cutoffs established for rilpivirine (2.5-FC) and the effect of mutation combinations on rilpivirine phenotype. Results Of the 100 samples from individuals on failing antiretroviral therapy, 69 had 2.5- to 75-fold decreased susceptibility to rilpivirine and 11 had >75-fold resistance. Rilpivirine resistance was strongly associated with K103N especially in combination with other rilpivirine-associated mutations. Conclusion The frequently observed cross-resistance of HIV-1 suggests that the preventive efficacy of TMC278LA pre-exposure prophylaxis could be compromised by transmission of HIV-1 from individuals with failure of first-line non-nucleoside reverse transcriptase inhibitor-containing antiretroviral therapy.
PIRATE: pediatric imaging response assessment and targeting environment

By combining the strengths of various imaging modalities, the multimodality imaging approach has potential to improve tumor staging, delineation of tumor boundaries, chemo-radiotherapy regime design, and treatment response assessment in cancer management. To address the urgent needs for efficient tools to analyze large-scale clinical trial data, we have developed an integrated multimodality, functional and anatomical imaging analysis software package for target definition and therapy response assessment in pediatric radiotherapy (RT) patients. Our software provides quantitative tools for automated image segmentation, region-of-interest (ROI) histogram analysis, spatial volume-of-interest (VOI) analysis, and voxel-wise correlation across modalities. To demonstrate the clinical applicability of this software, histogram analyses were performed on baseline and follow-up 18F-fluorodeoxyglucose (18F-FDG) PET images of nine patients with rhabdomyosarcoma enrolled in an institutional clinical trial at St. Jude Children's Research Hospital. In addition, we combined 18F-FDG PET, dynamic-contrast-enhanced (DCE) MR, and anatomical MR data to visualize the heterogeneity in tumor pathophysiology with the ultimate goal of adaptive targeting of regions with high tumor burden. Our software is able to simultaneously analyze multimodality images across multiple time points, which could greatly speed up the analysis of large-scale clinical trial data and validation of potential imaging biomarkers.
Receiver bias and the acoustic ecology of aye-ayes (Daubentonia madagascariensis)

The aye-aye is a rare lemur from Madagascar that uses its highly specialized middle digit for percussive foraging. This acoustic behavior, also termed tap-scanning, produces dominant frequencies between 6 and 15 kHz. An enhanced auditory sensitivity to these frequencies raises the possibility that the acoustic and auditory specializations of aye-ayes have imposed constraints on the evolution of their vocal signals, especially their primary long-distance vocalization, the screech. Here we explore this concept, termed receiver bias, and suggest that the dominant frequency of the screech call (~2.7 kHz) represents an evolutionary compromise between the opposing adaptive advantages of long-distance sound propagation and enhanced detection by conspecific receivers.