Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning-Based Cost Functions for 3-D and 4-D Multi-Surface Multi-Object Segmentation of Knee MRI: Data From the Osteoarthritis Initiative

A fully automated knee magnetic resonance imaging (MRI) segmentation method to study osteoarthritis (OA) was developed using a novel hierarchical set of random forests (RF) classifiers to learn the appearance of cartilage regions and their boundaries. A neighborhood approximation forest is used first to provide contextual feature to the second-level RF classifier that also considers local features and produces location-specific costs for the layered optimal graph image segmentation of multiple objects and surfaces (LOGISMOS) framework. Double-echo steady state MRIs used in this paper originated from the OA Initiative study. Trained on 34 MRIs with varying degrees of OA, the performance of the learning-based method tested on 108 MRIs showed significant reduction in segmentation errors (<inline-formula> <tex-math notation="LaTeX">${p}<\textsf {0.05}$ </tex-math></inline-formula>) compared with the conventional gradient-based and single-stage RF-learned costs. The 3-D LOGISMOS was extended to longitudinal-3-D (4-D) to simultaneously segment multiple follow-up visits of the same patient. As such, data from all time-points of the temporal sequence contribute information to a single optimal solution that utilizes both spatial 3-D and temporal contexts. 4-D LOGISMOS validation on 108 MRIs from baseline, and 12 month follow-up scans of 54 patients showed significant reduction in segmentation errors (<inline-formula> <tex-math notation="LaTeX">${p}<\textsf {0.01}$ </tex-math></inline-formula>) compared with 3-D. Finally, the potential of 4-D LOGISMOS was further explored on the same 54 patients using five annual follow-up scans demonstrating a significant improvement of measuring cartilage thickness (<inline-formula> <tex-math notation="LaTeX">${p}<\textsf {0.01}$ </tex-math></inline-formula>) compared with the sequential 3-D approach.
Molecular characterization and expression analysis of secretory immunoglobulin M (IgM) heavy chain gene in rohu, Labeo rohita

Abstract Immunoglobulin M (IgM) is the major isotype among teleost immunoglobulins. The present study was aimed to explore IgM heavy chain gene and its expression profile in rohu. Full-length IgM heavy chain cDNA of rohu consisted of 1994 bp encoding a polypeptide of 576 amino acid residues including a leader peptide, variable (VH) and constant (CH1–CH2–CH3–CH4) domains confirming the secretory form of IgM. The sequence carries conserved residues such as cysteine, tryptophan and amino acid motifs like ‘YYCAR’ and ‘FDYWGKGT–VTV–S’. The predicted 3 D model confirmed various domains of rohu IgM heavy chain. Phylogenetic tree analysis revealed that IgM heavy chain gene of rohu shared the same cluster with that of other cyprinid fishes. Tissue distribution analysis showed the predominant level of IgM heavy chain gene expression in kidney, spleen and intestine. IgM heavy chain gene expression in rohu kidney was found to be up-regulated and reached a maximum at 7 days post-challenge with Aeromonas hydrophila. These findings demonstrate the first report of full-length secretory IgM heavy chain gene in rohu. Besides, IgM heavy chain gene was highly expressed in major lymphoid tissues and bacterial challenge influenced its expression which further confirmed its role in the adaptive humoral immune response.
Adapting crops, landscapes, and food choices: Patterns in the dispersal of domesticated plants across Eurasia

Abstract After the domestication of plants and animals, the subsequent spread of agriculture represented a process of adaptation of both species and landscapes. Crop species moved beyond their original ecological limits, and their range expansion, when successful, was generally the result of adaptive post-domestication genetic changes on the part of the plants, human-induced changes in agricultural landscapes, and the dynamics of cultural food choice. This chapter explores the patterns by which agriculture became established as a consequence of the diffusion of domesticated plants (and sometimes people), as well as the ways in which agricultural systems were gradually transformed through the diversification of crop packages. Comparisons from across Eurasia are drawn to identify general patterns in crop dispersal, with three categories playing the largest role in the diffusion of grain-based agriculture. These agricultural systems are discussed and their modes of diffusion, stories of collapse, and examples of new adaptations on the part of the crops and agricultural systems detailed. Keywords : Agriculture, Neolithic, domestication, cuisine, archaeobotany INTRODUCTION Agriculture is widely regarded as one of the key changes in ecological and economic systems in the history of Homo sapiens (Diamond 2002; Bellwood 2005; Barker 2006; Smith and Zeder 2013). There is no doubt that agriculture set in motion increases in human population density and the transformation of environments, from biomes to ‘anthromes’ (sensu Ellis 2011). Over the long-term, land-use intensified primarily through agriculture, supporting denser populations and increasing regional carrying capacity by supporting more people from less land (Ellis et al. 2013). In this regard there should be little surprise that anthropologists and archaeologists have expended considerable effort on the study of agricultural origins, although more often than not this has focused on the search for pristine origins – those relatively few instances in which hunter-gatherers became farmers by domesticating plants and animals that were wild in their environment. As archaeological research and biological studies of wild progenitors have progressed, the number of recognized centres of origins has expanded from half a dozen or less, to close to ten, and perhaps even twenty or more (Fuller 2010; Larson et al. 2014). Nevertheless, it is undeniable that for the majority of the planet, agriculture was introduced from elsewhere and was based on plants and animals introduced as domesticates.
The success of the diversified farm : resource-based view

Farms and rural areas have many specific valuable resources that can be used to create non-agricultural products and services. Most of the research regarding on-farm diversification has hitherto concentrated on business start-up or farm survival strategies. Resource allocation and also financial success have not been the primary focus of investigations as yet. In this study these specific topics were investigated i.e. resource allocation and also the financial success of diversified farms from a farm management perspective. The key question addressed in this dissertation, is how tangible and intangible resources of the diversified farm affect the financial success. This studys theoretical ackground deals with resource-based theory, and also certain themes of the theory of learning organisation and other decision-making theories. Two datasets were utilised in this study. First, data were collected by postal survey in 2001 (n = 663). Second, data were collected in a follow-up survey in 2006 (n = 439). Data were analysed using multivariate data analyses and path analyses. The study results reveal that, diversified farms performed differently. Success and resources were linked. Professional and management skills affected other resources, and hence directly or indirectly influenced success per se. In the light of empirical analyses of this study, tangible and intangible resources owned by the diversified farm impacted on its financial success. The findings of this study underline the importance of skills and networks for entrepreneur(s). Practically speaking all respondents of this study used either agricultural resources for non-farm businesses or non-farm resources for agricultural enterprises. To share resources in this way was seen as a pragmatic opportunity recognised by farmers. One of the downsides of diversification might be the phenomenon of over-diversification, which can be defined as the situation in which a farm diversifies beyond its optimal limit. The empirical findings of this study reveal that capital and labour resource constrains did have adverse effects on financial success. The evidence indicates that farms that were capital and labour resource constrained in 2001 were still less profitable than their no problems counterparts five years later. ;
Citizen Science: Public Participation in Environmental Research

Foreword by Richard Louv Notes on Contributors AcknowledgmentsIntroduction: Why Citizen Science? by Janis L. Dickinson and Rick BonneyPart I. The Practice of Citizen Science1. Overview of Citizen Science by Rick Bonney and Janis L. Dickinson2. Projects and Possibilities: Lessons from Citizen Science ProjectsFrom Backyard Observations to Continent-Wide Trends: Lessons from the First Twenty-Two Years of Project FeederWatch by David N. BonterMonitoring Monarchs: Citizen Science and a Charismatic Insect by Karen S. OberhauserNeighborhood Nestwatch: Mentoring Citizens in the Urban Matrix by Peter P. Marra and Robert ReitsmaProject BudBurst: Citizen Science for All Seasons by Sandra Henderson, Dennis L. Ward, Kirsten K. Meymaris, Paul Alaback, and Kayri Havens3. Using Bioinformatics in Citizen Science by Steve Kelling4. Growing the Base for Citizen Science: Recruiting and Engaging Participants by Miyoko Chu, Patricia Leonard, and Flisa Stevenson5. What Is Our Impact? Toward a Unified Framework for Evaluating Outcomes of Citizen Science Participation by Tina Phillips, Rick Bonney, and Jennifer L. ShirkPart II. Impacts of Citizen Science on Conservation Research6. The Opportunities and Challenges of Citizen Science as a Tool for Ecological Research by Caren B. Cooper, Wesley M. Hochachka, and Andre A. Dhondt7. Widening the Circle of Investigation: The Interface between Citizen Science and Landscape Ecology by Benjamin Zuckerberg and Kevin McGarigal8. Using Data Mining to Discover Biological Patterns in Citizen Science Observations by Daniel Fink and Wesley M. Hochachka9. Developing a Conservation Research Program with Citizen Science by Ralph S. Hames, James D. Lowe, and Kenneth V. Rosenberg10. Citizens, Science, and Environmental Policy: A British Perspective by Jeremy J. D. GreenwoodPart III. Educational, Social, and Behavioral Aspects of Citizen Science11. Cognitive Considerations in the Development of Citizen Science Projects by Rebecca C. Jordan, Joan G. Ehrenfeld, Steven A. Gray, Wesley R. Brooks, David V. Howe, and Cindy E. Hmelo-Silver12. Who Poses the Question? Using Citizen Science to Help K-12 Teachers Meet the Mandate for Inquiry by Nancy M. Trautmann, Jennifer L. Shirk, Jennifer Fee, and Marianne E. Krasny13. A Gateway to Science for All: Celebrate Urban Birds by Karen Purcell, Cecilia Garibay, and Janis L. Dickinson14. Children and Nature: Following the Trail to Environmental Attitudes and Behavior by Nancy M. Wells and Kristi S. Lekies15. Internet-Based Social Networking and Collective Action Models of Citizen Science: Theory Meets Possibility by Heather A. Triezenberg, Barbara A. Knuth, Y. Connie Yuan, and Janis L. Dickinson16. A Role for Citizen Science in Disaster and Conflict Recovery and Resilience by Keith G. Tidball and Marianne E. KrasnyAfterword by John W. FitzpatrickLiterature Cited Index
Spontaneous Bone Bed Formation in Cochlear Implantation Using the Subperiosteal Pocket Technique

Objective To show evidence of spontaneous bone pocket formation using the subperiosteal pocket technique for cochlear implantation surgery. Study Design Clinical capsule report. Setting University hospital. Patients We evaluated 8 pediatric revision cochlear implant patients who had previously undergone cochlear implantation using the subperiosteal pocket technique. The time between primary and revision surgery varied between 5 and 54 months. Results Spontaneous bone bed formation for the internal receiver stimulator and its electrodes was observed during revision surgeries in all patients. Conclusion The subperiosteal pocket technique for cochlear implantation does not require pockets to be drilled in the skull, unlike the standard technique, because bone beds form spontaneously.
Oxidative Stress in the Pathogenesis of Preeclampsia (44447)

The etiology and pathogenesis of the pregnancy syndrome preeclampsia remain poorly understood. There is substantial evidence to suggest that the diverse manifestations of preeclampsia, including altered vascular reactivity, vasospasm, and discrete pathology in many organ systems, are derived from pathologic changes within the maternal vascular endothelium. With the theme of endothelial cell dysfunction emphasized, this review focuses on the role of oxidative stress (an imbalance favoring oxidant over antioxidant forces) in the pathogenesis of preeclampsia. Data are summarized regarding 1) the role of the placenta in preeclampsia; 2) evidence and mechanisms of oxidative stress in the preeclampsia placenta; 3) markers of oxidative stress in the maternal circulation; and 4) the potential role of maternal dyslipidemia in generation of oxidative stress. A recurrent theme is that free radical reactions, promoted by “cross-talk” between the diseased placenta and maternal dyslipidemia, promote a vicious cycle of events that make cause and effect difficult to distinguish but likely contribute to the progression of preeclampsia.
On the Simon Cipher 4-block key schedule as a hash

In this paper, we explore the use of the Simon Cipher 4-block key expansion as the basis for an unkeyed hash function that is target toward RFID and IoT applications. A modified Simon Cipher key expansion is used to create a construction that can be implemented to operate independently from, or concurrently when the Simon Cipher is used as an encryption engine.
Differential Sensitivity between Fks1p and Fks2p against a Novel β-1,3-Glucan Synthase Inhibitor, Aerothricin1*

Fks1p and Fks2p are catalytic subunits of β-1,3-glucan synthase, which synthesize β-1,3-glucan, a main component of the cell wall in Saccharomyces cerevisiae. Although Fks1p and Fks2p are highly homologous, sharing 88.1% identity, it has been shown that Fks2p is more sensitive than Fks1p to one of echinocandin derivatives, which inhibits β-1,3-glucan synthase activity. Here we show a similar differential sensitivity between Fks1p and Fks2p to a novel β-1,3-glucan synthase inhibitor, aerothricin1. To investigate the molecular mechanism of this differential sensitivity, we constructed a series of chimeric genes ofFKSs and examined their sensitivity to aerothricin1. As a result, it was shown that a region around the fourth extracellular domain of Fks2p, containing 10 different amino acid residues from those of Fks1p, provided Fks1p aerothricin1 sensitivity when the region was replaced with a corresponding region of Fks1p. In order to identify essential amino acid residues responsible for the sensitivity, each of the 10 non-conserved amino acids of Fks1p was substituted into the corresponding amino acid of Fks2p by site-directed mutagenesis. Surprisingly, only one amino acid substitution of Fks1p (K1336I) conferred Fks1p hypersensitivity to aerothricin1. On the other hand, reverse substitution of the corresponding amino acid of Fks2p (I1355K) resulted in loss of hypersensitivity to aerothricin1. These results suggest that the 1355th isoleucine of Fks2p plays a key role in aerothricin1 sensitivity.
MapSQ: A Plugin-based MapReduce Framework for SPARQL Queries on GPU

In this paper, we present a plugin-based framework (MapSQ) with three parts for SPARQL queries utilizing high-performance of GPU to accelerate answering in a convenient way. Selector chooses suitable join order according to characteristics of data and queries. Executor answers subqueries and returns intermediate solutions and GPU Computing obtains the join result of intermediate solutions through MapReduce. Finally, we evaluate MapSQ bulit on gStore and RDF-3X on the LUBM benchmark and YAGO datasets (over 200 million triples). The experimental results show that MapSQ significantly improves the performance of SPARQL query engines with speedup up to 33.
Industrial Growth and Wage Structure: An Inter-Regional Analysis

The structure of wages and wage determinants has always received attention in economic theories and policies. During the liberalized era, despite labour productivity, market based policies have gained importance in determining the wages. In the present study, the following issues are addressed: (a) How far the present pattern of industrial growth is responsible for the changing wage structure? , (b) Does all the states of India follow the similar wage structure irrespective of their development levels? , and (c) To what extent the structure of industrial growth and policies determine the wage share, average wage and wage disparity? The study undertakes a regional level approach. With the help of industry level data collected from Annual Survey of Industries, the study examines the structural changes in manufacturing industries after liberalization, links the productivity with wages and finds the regional wise differences in wage structure. The variations in wage share, average wage and wage disparity are estimated with the help of ordinary least squares method.
Projections from the upper lumbar cord to the cerebellar nuclei in the rat, studied by anterograde axonal tracing

The spinocerebellar tracts arising from the upper lumbar cord consist of the dorsal and the ventral spinocerebellar tracts (DSCT and VSCT), which ascend ipsilaterally and contralaterally, respectively. By using anterograde labeling with biotinylated dextran in the rat, this study examined whether the lumbar DSCT and the VSCT project to the cerebellar nuclei. Injections of the tracer were made unilaterally at levels between the L1 and L3 segments, with diffusion to either a rostral or a caudal segment. The injections resulted in bilateral labeling of axon terminals in the cerebellar nuclei. In the medial nucleus, labeled terminals were distributed in medial, ventral, and ventrolateral parts of the middle subdivision and ventral parts of the caudomedial subdivision. In the anterior interpositus nucleus, they were distributed in medial and dorsomedial parts throughout the rostrocaudal extent. Labeled terminals were seen within the dorsomedial crest region. In the posterior interpositus nucleus, labeled terminals were seen in the rostromedial extension, the caudomedial part, and the caudal pole. Labeled terminals were seen in the hilus and the ventral part of the lateral nucleus. Projections of the DSCT and the VSCT to these regions were confirmed after tracer injections preceded by sectioning of either tract. Both tracts projected bilaterally, but the DSCT projected mainly ipsilaterally. The present study suggests that the spinocerebellar tracts originating from the upper lumbar cord (the lumbar DSCT and the VSCT) project to specific areas of the cerebellar nuclei to transmit information about the peripheral and central events during the movement of hindlimbs. J. Comp. Neurol. 412:633–648, 1999. © 1999 Wiley‐Liss, Inc.
THE USE OF TELESCOPING SPATIAL SCALES TO CAPTURE INSHORE TO SLOPE DYNAMICS IN MARINE ECOSYSTEM MODELING

Abstract Ecosystem processes function at many scales, and capturing these processes is a challenge for ecosystem models. Nevertheless, it is a necessary step for considering many management issues pertaining to shelf and coastal systems. In this paper, we explore one method of modeling large areas with a focus at a range of scales. We develop an ecosystem model that can be used for strategic management decision support by modeling the waters off southeastern Australia using a polygon telescoping approach, which incorporates fine‐scale detail at the coastal zone, increasing in scale to a very coarse scale in the offshore areas. This telescoping technique is a useful tool for incorporating a wide range of habitats at different scales into a single model.
Distillation: A light-weight data separation design to boost performance of NVDIMM main memory

In the big data era, data-intensive applications have growing demand for the capacity of DRAM main memory, but the frequent DRAM refresh, high leakage power, and high unit cost bring serious design issues on scaling up DRAM capacity. To address this issue, NVDIMM, which is a hybrid memory module, becomes a possible alternative to replace DRAM as main memory in some data-intensive applications. NVDIMM that consists of a small-sized high-speed DRAM and a large-sized low-cost non-volatile memory (i.e., flash memory) has the serious performance issue on accessing data stored in the flash memory because of the huge performance gap between DRAM and flash memory. However, there is no or limited room to adopt a complex caching algorithm for using DRAM as the cache of flash memory in NVDIMM main memory because a complex caching algorithm itself would already cause too much performance degradation on handling each request to NVDIMM main memory. In this paper, we present a light-weight data separation design to boost NVDIMM performance with limited data separation overhead for reducing the data accesses to flash memory. A series of experiments was conducted based on popular benchmarks, and the results demonstrate that the proposed design can effectively improve the performance of NVDIMM main memory.
Transgenerational sperm DNA methylation epimutation developmental origins following ancestral vinclozolin exposure

ABSTRACT A number of environmental factors from nutrition to toxicants have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. This requires alterations in the germline (sperm or egg) epigenome. Previously, the agricultural fungicide vinclozolin was found to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs) termed epimutations that help mediate this epigenetic inheritance. The current study was designed to investigate the developmental origins of the transgenerational DMRs during gametogenesis. Male control and vinclozolin lineage F3 generation rats were used as a source of embryonic day 13 (E13) primordial germ cells, embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus vinclozolin lineage samples were determined for each developmental stage. The top 100 statistically significant DMRs for each stage were compared. The developmental origins of the caudal epididymal sperm DMRs were assessed. The chromosomal locations and genomic features of the different stage DMRs were investigated. In addition, the DMR associated genes were identified. Previous studies have demonstrated alterations in the DMRs of primordial germ cells (PGCs). Interestingly, the majority of the DMRs identified in the current study for the caudal sperm originated during the spermatogenic process in the testis. A cascade of epigenetic alterations initiated in the PGCs appears to be required to alter the epigenetic programming during spermatogenesis to modify the sperm epigenome involved in the transgenerational epigenetic inheritance phenomenon.