Miracle-dz/UniFAR-FTUs huggingface dataset:
Prognostic Factors on Overall Survival in Lymph Node Negative Gastric Cancer Patients Who Underwent Curative Resection

Purpose To assess independent prognostic factors for lymph node-negative metastatic gastric cancer patients following curative resection is valuable for more effective follow-up strategies. Materials and Methods Among 1,874 gastric cancer patients who received curative resection, 967 patients were lymph node-negative. Independent prognostic factors for overall survival in lymph node-negative gastric cancer patients grouped by tumor invasion depth (early gastric cancer versus advanced gastric cancer) were explored with univariate and multivariate analyses. Results There was a significant difference in the distribution of recurrence pattern between lymph node-negative and lymph node-positive group. In the lymph node-negative group, the recurrence pattern differed by the depth of tumor invasion. In univariate analysis for overall survival of the early gastric cancer group, age, macroscopic appearance, histologic type, venous invasion, lymphatic invasion, and carcinoembryonic antigen level were significant prognostic factors. Multivariate analysis for these factors showed that venous invasion (hazard ratio, 6.695), age (≥59, hazard ratio, 2.882), and carcinoembryonic antigen level (≥5 ng/dl, hazard ratio, 3.938) were significant prognostic factors. Multivariate analysis of advanced gastric cancer group showed that depth of tumor invasion (T2 versus T3, hazard ratio, 2.809), and age (hazard ratio, 2.319) were prognostic factors on overall survival. Conclusions Based on our results, independent prognostic factors such as venous permeation, carcinoembryonic antigen level, and age, depth of tumor invasion on overall survival were different between early gastric cancer and advanced gastric cancer group in lymph node-negative gastric cancer patients. Therefore, we are confident that our results will contribute to planning follow-up strategies.
Operator splitting for the KdV equation

We provide a new analytical approach to operator splitting for equations of the type u t = Au + B(u), where A is a linear operator and B is quadratic. A particular example is the Korteweg-de Vries (KdV) equation u t - uu x + u xxx = 0. We show that the Godunov and Strang splitting methods converge with the expected rates if the initial data are sufficiently regular.
Stability selection

Summary. Estimation of structure, such as in variable selection, graphical modelling or cluster analysis, is notoriously difficult, especially for high dimensional data. We introduce stability selection. It is based on subsampling in combination with (high dimensional) selection algorithms. As such, the method is extremely general and has a very wide range of applicability. Stability selection provides finite sample control for some error rates of false discoveries and hence a transparent principle to choose a proper amount of regularization for structure estimation. Variable selection and structure estimation improve markedly for a range of selection methods if stability selection is applied. We prove for the randomized lasso that stability selection will be variable selection consistent even if the necessary conditions for consistency of the original lasso method are violated. We demonstrate stability selection for variable selection and Gaussian graphical modelling, using real and simulated data.
Adjective-Noun Placement Variation in French Twitter Corpora

French written and spoken corpora reveal that variation of adjective-noun placement occurs more often within written corpora than in spoken ones (Lightfoot, 1979; Prévost, 2009; Thuilier, 2013). I examine adjective lemma variation of placement, adjective categories, frequency, and syllable length as a means of assessing current Twitter trends of adjective placement. In this preliminary study, a cross-section of 30 adjective lemmas within a corpus of approximately 6,000 French tweets demonstrates that parallels exist between the usage of adjectives on Twitter and norms of spoken French.
Occupants’ Perceptions of Amenity and Efficiency for Verification of Spatial Design Adequacy

The best spatial design condition to satisfy the occupancy needs of amenity and efficiency is determined through analyzing the spatial design adequacy (SDA). In this study, the relationship between the space design elements and space on future occupants’ perception are analyzed. The thirty-three participants reported their self-evaluated SDA that describes the quality of eight alternative housing living rooms with different spatial factors. The occupants were guided through the perception processing elaboration in order for them to evaluate the actual perception in the real space. The findings demonstrated that the spatial size (e.g., width, depth, and height) is significantly correlated with the overall satisfaction of amenity. It is also found that the spatial shape (e.g., the width-to-depth ratio, the height-to-area ratio, and room shape) may significantly influence the overall satisfaction of efficiency. The findings also demonstrate that the causal relationship between the spatial factors and space is clearly present in the occupants’ perception, reflecting the time-sequential characteristics of the actual experience divided into amenity and efficiency. This result indicates that the correlation between the spatial factors and space of SDA under the occupants’ perception processing elaboration can be a useful guide to predict the occupancy satisfaction of amenity and efficiency in real spaces.
Linking Macroscopic with Microscopic Neuroanatomy Using Synthetic Neuronal Populations

Dendritic morphology has been shown to have a dramatic impact on neuronal function. However, population features such as the inherent variability in dendritic morphology between cells belonging to the same neuronal type are often overlooked when studying computation in neural networks. While detailed models for morphology and electrophysiology exist for many types of single neurons, the role of detailed single cell morphology in the population has not been studied quantitatively or computationally. Here we use the structural context of the neural tissue in which dendritic trees exist to drive their generation in silico. We synthesize the entire population of dentate gyrus granule cells, the most numerous cell type in the hippocampus, by growing their dendritic trees within their characteristic dendritic fields bounded by the realistic structural context of (1) the granule cell layer that contains all somata and (2) the molecular layer that contains the dendritic forest. This process enables branching statistics to be linked to larger scale neuroanatomical features. We find large differences in dendritic total length and individual path length measures as a function of location in the dentate gyrus and of somatic depth in the granule cell layer. We also predict the number of unique granule cell dendrites invading a given volume in the molecular layer. This work enables the complete population-level study of morphological properties and provides a framework to develop complex and realistic neural network models.
Climate drivers of seed production in Picea engelmannii and response to warming temperatures in the southern Rocky Mountains

Seed production by Picea engelmannii was monitored at 13 sites distributed across a ˜670 m elevation gradient for 40 years. Time series of annual seed output was investigated for evidence of masting behaviour and trends in seed abundance over time. We used regression models in a likelihood framework to examine climate effects on seed production for critical periods in the species' reproductive cycle. We rigorously evaluated the performance of two gridded climate data sets, PRISM and TopoWx, before using associated variables as predictors in the seed models. Seed production at these sites does not strictly conform to the classic masting concept. Seed abundance was highly variable over time and strongly synchronized among sites, but mast years could not be objectively identified due to intermediate levels of seed output. Model results indicate that climate conditions across multiple years cumulatively determine reproductive output. High seed rain is associated with elevated summer temperatures in the year that seeds are dispersed, low spring snowfall in the year preceding seed dispersal when buds are initiated, and reduced spring snowfall in a so‐called priming year two years prior to seed dispersal. Low spring precipitation putatively increases growing season length and resource accumulation in seed trees. Linear models identified significant positive trends in seed output over time. Anomalous aridity and summer warmth in the latter half of the study period were highly favourable for seed production and were associated with increases in seed abundance. Synthesis. The increases in seed output observed in this study may promote population fitness of P. engelmannii in the face of changing climate regimes and increasing frequencies of fire‐ and insect‐related tree mortality in the Rocky Mountains. Since this species lacks a persistent seed bank, re‐colonization of disturbed areas or dispersal to shifting habitats depends on adequate production of seed by surviving trees, which according to these analyses may be moderately enhanced by current climate trends. However, some evidence also indicates that increases in seed output will ultimately be constrained by threshold high temperatures in the seed maturation year.
Combining filtering and statistical methods for anomaly detection

In this work we develop an approach for anomaly detection for large scale networks such as that of an enterprize or an ISP. The traffic patterns we focus on for analysis are that of a network-wide view of the traffic state, called the traffic matrix. In the first step a Kalman filter is used to filter out the "normal" traffic. This is done by comparing our future predictions of the traffic matrix state to an inference of the actual traffic matrix that is made using more recent measurement data than those used for prediction. In the second step the residual filtered process is then examined for anomalies. We explain here how any anomaly detection method can be viewed as a problem in statistical hypothesis testing. We study and compare four different methods for analyzing residuals, two of which are new. These methods focus on different aspects of the traffic pattern change. One focuses on instantaneous behavior, another focuses on changes in the mean of the residual process, a third on changes in the variance behavior, and a fourth examines variance changes over multiple timescales. We evaluate and compare all of these methods using ROC curves that illustrate the full tradeoff between false positives and false negatives for the complete spectrum of decision thresholds.
Total elbow arthroplasty with use of a nonconstrained humeral component inserted without cement in patients who have rheumatoid arthritis.

BACKGROUND Most total elbow prostheses that are currently in use require cement for fixation of each component. We developed a new (type-5) prosthesis that does not need cement for fixation. METHODS The humeral component is made of cobalt-chromium alloy, and its stem is porous-coated with a plasma spray of titanium alloy. There are two options for the ulnar component: an all-polyethylene type and a metal-backed type with a porous-coated stem. Forty-three elbows in thirty-seven patients who had rheumatoid arthritis were treated with total elbow replacement arthroplasty with use of the type-5 prosthesis. The humeral component was implanted without cement in all elbows, whereas the ulnar component was implanted without cement in eleven elbows and was fixed with cement in the remaining thirty-two. The elbows were followed for an average of three years and ten months (range, two years and six months to five years and six months). RESULTS The clinical results were assessed according to a modification of the Mayo Clinic Performance Index. At the time of the latest follow-up, the overall result was excellent for six elbows, good for thirty-one, and fair for six. All elbows had been rated as poor before the operation. There was almost complete relief of pain in twenty-nine elbows and mild or occasional pain in the remaining fourteen. Flexion increased markedly, from an average of 104 degrees preoperatively to an average of 133 degrees postoperatively; this difference was highly significant (p < 0.001, Student t test). In contrast, extension (flexion contracture) worsened slightly, from an average of 38 degrees preoperatively to an average of 42 degrees postoperatively; this difference was significant (p < 0.05). There was one postoperative dislocation of the elbow, and ectopic bone formed in another, with recurrence of ankylosis. Both elbows had a reoperation, and a good result eventually was obtained. There were no instances of postoperative infection or neuropathy of the ulnar nerve. Radiographically, there were no radiolucent lines at the bone-metal interface of any of the humeral or ulnar stems that had been implanted without cement, suggesting solid fixation by osseointegration. CONCLUSIONS The results of total elbow arthroplasty with use of this prosthesis appear promising. There was a high rate of relief of pain as well as of restoration of adequate function in patients in whom the elbow was severely affected by rheumatoid arthritis.
Azido-Containing Diketo Acid Derivatives Inhibit Human Immunodeficiency Virus Type 1 Integrase In Vivo and Influence the Frequency of Deletions at Two-Long-Terminal-Repeat-Circle Junctions

ABSTRACT We previously found that azido-containing β-diketo acid derivatives (DKAs) are potent inhibitors of human immunodeficiency virus type 1 (HIV-1) integrase (IN) (X. Zhang et al., Bioorg. Med. Chem. Lett., 13:1215-1219, 2003). To characterize the intracellular mechanisms of action of DKAs, we analyzed the antiviral activities of two potent azido-containing DKAs with either a monosubstitution or a disubstitution of azido groups, using single- and multiple-replication-cycle assays. Both azido-containing DKAs significantly inhibited HIV-1 infection in 293T, CEM-SS, and H9 cells (50% inhibitory concentration = 2 to 13 μM) and exhibited low cytotoxicity (50% cytotoxic concentration = 60 to 600 μM). Inhibition of HIV-1 IN in vivo was demonstrated by the observation that previously described L-708,906 resistance mutations in HIV-1 IN (T66I and T66I/S153Y) also conferred resistance to the azido-group-containing DKAs. In vitro assays and in vivo analysis indicated that the DKAs did not significantly inhibit the 3′ processing and selectively inhibited the strand transfer reaction. In addition, quantitative PCR indicated that two-long-terminal-repeat (2-LTR) circles were elevated in the presence of the azido-containing DKAs, confirming that HIV-1 IN was the intracellular target of viral inhibition. To gain insight into the mechanism by which the DKAs increased 2-LTR-circle formation of 3′-processed viral DNAs, we performed extensive DNA sequencing analysis of 2-LTR-circle junctions. The results indicated that the frequency of deletions at the circle junctions was elevated from 19% for the untreated controls to 32 to 41% in the presence of monosubstituted (but not disubstituted) DKAs. These results indicate that the structure of the DKAs can influence the extent of degradation of viral DNA ends by host nucleases and the frequency of deletions at the 2-LTR-circle junctions. Thus, sequencing analysis of 2-LTR-circle junctions can elucidate the intracellular mechanisms of action of HIV-1 IN inhibitors.
Porphyromonas gingivalis genes isolated by screening for epithelial cell attachment

Porphyromonas gingivalis is associated with chronic and severe periodontitis in adults. P. gingivalis and the other periodontal pathogens colonize and interact with gingival epithelial cells, but the genes and molecular mechanisms involved are unknown. To dissect the first steps in these interactions, a P. gingivalis expression library was screened for clones which bound human oral epithelial cells. Insert DNA from the recombinant clones did not contain homology to the P. gingivalis fimA gene, encoding fimbrillin, the subunit protein of fimbriae, but showed various degrees of homology to certain cysteine protease-hemagglutinin genes. The DNA sequence of one insert revealed three putative open reading frames which appeared to be in an operon. The relationship between P. gingivalis attachment to epithelial cells and the activities identified by the screen is discussed.
Integrating supply chain and network analyses: The study of netchains

This paper introduces the concept of netchain analysis. A netchain is a set of networks comprised of horizontal ties between firms within a particular industry or group, which are sequentially arranged based on vertical ties between firms in different layers. Netchain analysis interprets supply chain and network perspectives on inter-organisational collaboration with particular emphasis on the value creating and coordination mechanism sources. We posit that sources of value and coordination mechanisms correspond to particular and distinct types of interdependencies: pooled, sequential, and reciprocal. It is further argued that the recognition and accounting of these simultaneous interdependencies is crucial for a more advanced understanding of complex inter-organisational relations. The paper concludes with an analysis of a set of netchain configuration examples, including buyer-supplier relationships, information technology induced interorganization collaborations, and the introduction of the "macrohiera.
A simulation environment for multi-antenna software defined radio

This paper describes a generic simulation workbench for multiple antenna Software Defined Radio (SDR) systems in MATLAB or OCTAVE, for both Windows and Unix/Linux operating systems. The workbench is functionally modularized into blocks and sub-blocks with a common interface for the convenience of modification and reconfiguration. Currently, it accommodates a variety of transmission schemes, including single-carrier multiple-input multiple-output (MIMO), Orthogonal Frequency-Division Multiplexing (OFDM), multi-carrier MIMO, Wideband Code Division Multiple Access (WCDMA), filtered multitone (FMT), which have extensive applications in modern communication technologies, e.g., WLAN 802.11 a/b/g/n, WiMAX, UWB, 3G cellular network, ADSL, DVB, etc.
Glacio‐isostatic age modelling and Late Weichselian deglaciation of the Lögurinn basin, East Iceland

Knowledge of the glaciation of central East Iceland between 15 and 9 cal. ka BP is important for the understanding of the extent, retreat and dynamics of the Icelandic Ice Sheet. Crucially, it is not known if the key area of Fljótsdalur‐Úthérað carried a fast‐flowing ice stream during the Last Glacial Maximum; the timing and mode of deglaciation is unclear; and the history and ages of successive lake‐phases in the Lögurinn basin are uncertain. We use the distribution of glacial and fluvioglacial deposits and gradients of former lake shorelines to reconstruct the glaciation and deglaciation history, and to constrain glacio‐isostatic age modelling. We conclude that during the Last Glacial Maximum, Fljótsdalur‐Úthérað was covered by a fast‐flowing ice stream, and that the Lögurinn basin was deglaciated between 14.7 and 13.2 cal. ka BP at the earliest. The Fljótsdalur outlet glacier re‐advanced and reached a temporary maximum extent on two separate occasions, during the Younger Dryas and the Preboreal. In the Younger Dryas, about 12.1 cal. ka BP, the outlet glacier reached the Tjarnarland terminal zone, and filled the Lögurinn basin. During deglaciation, a proglacial lake formed in the Lögurinn basin. Through time, gradients of ice‐lake shorelines increased as a result of continuous but non‐uniform glacio‐isostatic uplift as the Fljótsdalur outlet glacier retreated across the Valþjófsstaður terminal zone. Changes in shoreline gradients are defined as a function of time, expressed with an exponential equation that is used to model ages of individual shorelines. A glaciolacustrine phase of Lake Lögurinn existed between 12.1 and 9.1 cal. ka BP; as the ice retreated from the basin catchment, a wholly lacustrine phase of Lake Lögurinn commenced and lasted until about 4.2 cal. ka BP when neoglacial ice expansion started the current glaciolacustrine phase of the lake.
EXPERIMENTAL POLYMICROBIAL PERITONITIS-ASSOCIATED TRANSCRIPTIONAL REGULATION OF MURINE ENDOGENOUS RETROVIRUSES

Despite advancements in understanding the pathophysiology of sepsis, clinical outcomes are variable, and the mortality rate remains high among patients. We investigated whether expression of murine endogenous retroviruses (MuERVs), constituting ∼10% of the mouse genome, is differentially regulated in response to sepsis-elicited stress signals. ICR mice were subjected to cecal ligation and puncture, and MuERV expression was examined. There was evident regulation (induced or repressed) of MuERV expression in the liver and lung after cecal ligation and puncture. In particular, expression of several variant transcripts was increased, primarily in the liver, at 12 and/or 48 h: nine splicing variants and one 5.06-kb nonspliced transcript. Four novel splicing signals were also identified. Six variant transcripts were presumed to be splicing products of the 5.06-kb transcript, whereas the other three were envelope variants transcribed from at least five MuERV loci. These findings demonstrate that expression of certain MuERVs, including their envelope subgenomic transcripts, are altered during the course of sepsis pathogenesis.
The Use of Robotic and Laparoscopic Surgical Stapling Devices During Minimally Invasive Colon and Rectal Surgery: A Comparison.

PURPOSE To date there exists no published study examining the safety and efficacy of the EndoWrist 45 (Intuitive Surgical, Inc.) robotic stapler. We compared outcomes between the robotic and comparable laparoscopic stapler in robotic-assisted colorectal procedures. MATERIALS AND METHODS We conducted a retrospective review of 93 patients who underwent robotic-assisted colorectal surgery at our institution from 2012 to 2014. Surgeries included left, sigmoid, subtotal and total colectomies, and low anterior rectal resections. Indications were malignancy and diverticular and inflammatory bowel disease. Preoperative demographics, intraoperative data, and postoperative outcomes were examined. Student's t-test and Fischer's exact used were appropriate. RESULTS Forty-five millimeters laparoscopic staplers were used in 58 cases, while the 45 mm robotic stapler was used in 35 cases. There was no difference in age (P = .651), gender (P = .832), or body mass index (P = .204) between groups. There was no difference in estimated blood loss (P = .524), operative time (P = .769), length of stay (P = .895), or complication rate (P = .778). The robotic stapler group had one anastomotic leak, while the laparoscopic stapler group had six (P = .705). There were more laparoscopic stapler fires (2.69) per patient than robotic stapler fires (1.86) (P = .001). The cost per patient for the laparoscopic group was $631.45 versus $473.28 for the robotic group (P = .001). CONCLUSION This is the first study to evaluate the robotic stapler. Advantages of the robotic stapler include large range of motion and 90° of articulation, which may provide a benefit when using the stapler in difficult areas like the pelvis. The robotic stapler has a comparable level of safety as a 45 mm laparoscopic stapler and is more cost effective.