Miracle-dz/UniFAR-FTUs huggingface dataset:
Mediastinal Nodal Involvement in Patients with Clinical Stage I Non–Small-Cell Lung Cancer: Possibility of Rational Lymph Node Dissection

Background: The aim of this study is to elucidate the optimal candidate of selective lymph node dissection (LND) that reduces the extent of mediastinal LND according to clinical information including radiological evaluation in primary non–small-cell lung cancer (NSCLC) patients. Methods: Eight hundred and seventy-six patients with clinical(c)-stage I NSCLC (adenocarcinoma and squamous cell carcinoma), who underwent complete surgical resection between January 2003 and December 2009 were included in this study. We elucidated the lymph node metastatic incidence and distribution according to the primary tumor lobe location and extracted the associated clinicopathological factors, especially thin-section computed tomographic findings, with mediastinal lymph node involvement. Results: The total incidence of mediastinal lymph node metastasis was 9.1%. There were no cases with hilar and mediastinal lymph node metastasis in ground glass opacity-predominant tumors. There was no significant association of clinical factors with subcarinal lymph node metastasis in right upper-lobe and left upper-division adenocarcinoma. An elevated preoperative serum carcinoembryonic antigen level (p < 0.001) showed significant associations with upper mediastinal lymph node metastasis in the patients with bilateral lower-lobe primary lung adenocarcinoma. Conclusions: It would be acceptable to perform selective LND in patients with c-stage I NSCLC with ground glass opacity- predominant tumor. Elevated serum carcinoembryonic antigen was associated with upper mediastinal lymph node involvement in lower-lobe primary lung adenocarcinoma with radiologically solid-predominant tumor. We should be careful when applying selective LND to patients with solid-predominant tumor, especially located in the lower lobe.
Mutagenesis of theN-(Deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine DNA Adduct in Mammalian Cells

Site-specifically modified oligodeoxynucleotides were used to investigate the mutagenic properties of a major cooked food mutagen-derived DNA adduct,N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo[4, 5-b]pyridine (dG-C8-PhIP). dG-C8-PhIP-modified oligodeoxynucleotides were prepared by reacting an oligodeoxynucleotide containing a single dG (5′-TCCTCCTX GCCTCTC, where X = C, A, G, or T) with N-acetoxy-PhIP. The unmodified and dG-C8-PhIP-modified oligomers were inserted into single-stranded phagemid vectors. These single-stranded vectors were transfected into simian kidney (COS-7) cells. The progeny plasmid obtained was used to transform Escherichia coli DH10B. When dC was at the 5′-flanking position to dG-C8-PhIP, preferential incorporation of dCMP, the correct base, was observed opposite the dG-C8-PhIP. Targeted G → T transversions were detected, along with lesser amounts of G → A transitions and G → C transversions. No mutations were detected for the unmodified vector. The influence of sequence context on the dG-C8-PhIP mutation frequency and spectrum was also explored. When the dC 5′-flanking base was replaced by dT, dA, or dG, the mutational spectra were similar to that observed with dC-flanking base. Higher mutational frequencies (28–30%) were observed when dC or dG was 5′ to dG-C8-PhIP. A lower mutational frequency (13%) was observed when dA was at the 5′ to the lesion. Single-base deletions were detected only when dG or dT flanked the adduct. We conclude that dG-C8-PhIP is mutagenic, generating primarily G → T transversions in mammalian cells. The mutational frequency and specificity of dG-C8-PhIP vary depending on the neighboring sequence context.
Prevalence of Cervical Enamel Projection and Its Impact on Furcation Involvement in Mandibular Molars: A Cone‐Beam Computed Tomography Study in Koreans

This study evaluated the prevalence of cervical enamel projections (CEPs) in mandibular molars, and analyzed the correlation between CEPs and furcation involvement (FI) based on cone‐beam computed tomography (CBCT) data in a Korean population. CBCT images obtained from March 2012 to August 2012 were analyzed. CEPs and FI on the buccal and lingual surface were classified in three‐dimensionally reconstructed images and cross‐sectional views, and the correlation between these two parameters was analyzed. In total, 982 teeth in 425 patients were analyzed. The overall prevalence rate of CEPs was 76% (71% and 27% on the buccal and lingual surfaces, respectively). Grade I CEPs were the most common, followed by CEPs of grades II and III. There was a statistically significant, but negligible correlation between the CEP grade and the degree of FI on the buccal and lingual surfaces. Within the limitations of this cross‐sectional study, a high prevalence of CEPs were found in a Korean population, but the role of CEPs in provoking FI appeared not to be decisive. Anat Rec, 299:379–384, 2016. © 2015 Wiley Periodicals, Inc.
Proofs as Relational Invariants of Synthesized Execution Grammars

The automatic verification of programs that maintain unbounded low-level data structures is a critical and open problem. Analyzers and verifiers developed in previous work can synthesize invariants that only describe data structures of heavily restricted forms, or require an analyst to provide predicates over program data and structure that are used in a synthesized proof of correctness. In this work, we introduce a novel automatic safety verifier of programs that maintain low-level data structures, named LTTP. LTTP synthesizes proofs of program safety represented as a grammar of a given program's control paths, annotated with invariants that relate program state at distinct points within its path of execution. LTTP synthesizes such proofs completely automatically, using a novel inductive-synthesis algorithm. We have implemented LTTP as a verifier for JVM bytecode and applied it to verify the safety of a collection of verification benchmarks. Our results demonstrate that LTTP can be applied to automatically verify the safety of programs that are beyond the scope of previously-developed verifiers.
Electronics for the BaBar central drift chamber

The central drift chamber for the BaBar detector at the SLAC B-factory is based on a hexagonal cell design with 7104 cells arranged in 40 layers and drift gas helium:isobutane (80%:20%). Performance optimization and integration requirements led to an electronics design that mounts the amplifier-discriminator and digitizing circuitry directly on the endplate. High channel density is achieved using a 4-channel custom amplifier-discriminator IC and an 8-channel custom CMOS TDC/FADC IC on a single circuit board. Data read from the front ends are multiplexed on 4 fiber optic links, and prompt trigger data are sent out continuously on 24 links. Analysis of cosmic ray data demonstrates that the electronics design meets the performance goals for the BaBar drift chamber. The final electronics were installed on the drift chamber in July, 1998. Installation of BaBar on beamline is scheduled for March, 1999.
Beneficial effects of creatine, CoQ10, and lipoic acid in mitochondrial disorders

Mitochondrial disorders share common cellular consequences: (1) decreased ATP production; (2) increased reliance on alternative anaerobic energy sources; and (3) increased production of reactive oxygen species. The purpose of the present study was to determine the effect of a combination therapy (creatine monohydrate, coenzyme Q10, and lipoic acid to target the above‐mentioned cellular consequences) on several outcome variables using a randomized, double‐blind, placebo‐controlled, crossover study design in patients with mitochondrial cytopathies. Three patients had mitochondrial encephalopathy, lactic acidosis, and stroke‐like episodes (MELAS), four had mitochondrial DNA deletions (three patients with chronic progressive external ophthalmoplegia and one with Kearns–Sayre syndrome), and nine had a variety of other mitochondrial diseases not falling into the two former groups. The combination therapy resulted in lower resting plasma lactate and urinary 8‐isoprostanes, as well as attenuation of the decline in peak ankle dorsiflexion strength in all patient groups, whereas higher fat‐free mass was observed only in the MELAS group. Together, these results suggest that combination therapies targeting multiple final common pathways of mitochondrial dysfunction favorably influence surrogate markers of cellular energy dysfunction. Future studies with larger sample sizes in relatively homogeneous groups will be required to determine whether such combination therapies influence function and quality of life. Muscle Nerve, 2006
Enabling Performance Evaluation Beyond 10 Gbps

Despite network monitoring and testing being critical for computer networks, current solutions are both extremely expensive and inflexible. This demo presents OSNT (www.osnt.org), a community-driven, high-performance, open-source traffic generator and capture system built on top of the NetFPGA-10G board which enables flexible network testing. The platform supports full line-rate traffic generation regardless of packet size across the four card ports, packet capture filtering and packet thinning in hardware and sub-msec time precision in traffic generation and capture, corrected using an external GPS device. Furthermore, it provides a software APIs to test the dataplane performance of multi-10G switches, providing a starting point for a number of different test cases. OSNT flexibility is further demonstrated through the OFLOPS-turbo platform: an integration of OSNT with the OFLOPS OpenFlow switch performance evaluation platform, enabling control and data plane evaluation of 10G switches. This demo showcases the applicability of the OSNT platform to evaluate the performance of legacy and OpenFlow-enabled networking devices, and demonstrates it using commercial switches.
Enhancement of Thiamine Biosynthesis in Oil Palm Seedlings by Colonization of Endophytic Fungus Hendersonia toruloidea

Thiamine, or vitamin B1 plays an indispensable role as a cofactor in crucial metabolic reactions including glycolysis, pentose phosphate pathway and the tricarboxylic acid cycle in all living organisms. Thiamine has been shown to play a role in plant adaptation toward biotic and abiotic stresses. The modulation of thiamine biosynthetic genes in oil palm seedlings was evaluated in response to root colonization by endophytic Hendersonia toruloidea. Seven-month-old oil palm seedlings were inoculated with H. toruloidea and microscopic analyses were performed to visualize the localization of endophytic H. toruloidea in oil palm roots. Transmission electron microscopy confirmed that H. toruloidea colonized cortical cells. The expression of thiamine biosynthetic genes and accumulation of total thiamine in oil palm seedlings were also evaluated. Quantitative real-time PCR was performed to measure transcript abundances of four key thiamine biosynthesis genes (THI4, THIC, TH1, and TPK) on days 1, 7, 15, and 30 in response to H. toruloidea colonization. The results showed an increase of up to 12-fold in the expression of all gene transcripts on day 1 post-inoculation. On days 7, 15, and 30 post-inoculation, the relative expression levels of these genes were shown to be downregulated. Thiamine accumulation was observed on day 7 post-colonization and subsequently decreased until day 30. This work provides the first evidence for the enhancement of thiamine biosynthesis by endophytic colonization in oil palm seedlings.
Dynamic Scheduling with Statistical Delay Guarantees and Traffic Dropping

This work studies the dynamic scheduling problems in wireless networks with delay-sensitive loss-tolerant users. The users' traffic satisfies some statistical delay constraints. Moreover, the traffic can be dropped but the dropping rates do not exceed some thresholds. We consider two scheduling scenarios. First, we study the problem to minimize the total transmission power while maintaining the minimum rates for the users. Then, we study the problem to maximize the minimum rate(s) of the users while constraining the maximum total power. We derive the optimal solutions for both scheduling problems. When the fading statistics are available, using the dual-gradient method, the optimal policies can be computed. When the fading statistics are unknown, this work proposes online scheduling algorithms using online time-averaging. The convergence and optimality of the proposed algorithm are guaranteed by the results in stochastic approximation theory.
Early treatment of a quetiapine and sertraline overdose with Intralipid® *

We describe the initial management and subsequent recovery of a 61 year‐old male patient following attempted suicide by oral ingestion of a potentially fatal overdose of quetiapine and sertraline. Intravenous Intralipid® was given soon after initiation of basic resuscitation. There was a rapid improvement in the patient’s level of consciousness. No other clinical signs of drug toxicity were observed. Intralipid may have reversed the deep coma associated with ingestion and prevented other manifestations of drug toxicity occurring, thus expediting this patient's recovery.
Finesse of silicon-based terahertz Fabry-Perot spectrometer

This paper considers factors that affect achievable finesse for a recently demonstrated silicon-based scanning Fabry- Perot transmission filter at millimeter and sub-millimeter wavelengths. The mirrors are formed by alternating quarter-wave optical thicknesses of silicon and air in the usual Bragg configuration. Fundamental loss by lattice and free carrier absorption are considered. Technological factors such as surface roughness, bowing, and misalignment are considered for various proposed manufacturing schemes.
ΔNp63 plays an anti-apoptotic role in ventral bladder development

The bladder, the largest smooth-muscle organ in the human body, is responsible for urine storage and micturition. P63, a homolog of the p53 tumor-suppressor gene, is essential for the development of all stratified epithelia, including the bladder urothelium. The N-terminal truncated isoform of p63, ΔNp63, is known to have anti-apoptotic characteristics. We have established that ΔNp63 is not only the predominant isoform expressed throughout the bladder, but is also preferentially expressed in the ventral bladder urothelium during early development. We observed a host of ventral defects in p63-/- embryos, including the absence of the abdominal and ventral bladder walls. This number of ventral defects is identical to bladder exstrophy, a congenital anomaly exhibited in human neonates. In the absence of p63, the ventral urothelium was neither committed nor differentiated, whereas the dorsal urothelium was both committed and differentiated. Furthermore, in p63-/- bladders, apoptosis in the ventral urothelium was significantly increased. This was accompanied by the upregulation of mitochondrial apoptotic mediators Bax and Apaf1, and concurrent upregulation of p53. Overexpression ofΔ Np63γ and ΔNp63β in p63-/- bladder primary cell cultures resulted in a rescue, evidenced by significantly reduced expressions of Bax and Apaf1. We conclude that ΔNp63 plays a crucial anti-apoptotic role in normal bladder development.
A Mother's Attitude Towards her Infant and Child Behaviour Five Years Later

Objective: The relationship between maternal attitude to the infant at 6 months of age and behavioural outcomes at 5 years is explored, controlling for numerous demographic, child and psychosocial family factors. Method: Data was used from the Mater-University Study of Pregnancy, an Australian longitudinal study of over 7000 mothers and children followed from pregnancy to when the children were 5 years. Measures ranging from the key variables of maternal attitude and child behaviour as well as numerous confounders were dichotomised. Logistic regression analyses were performed to examine the relationship between maternal negative attitude toward the infant and clinically significant levels of child behaviour problems and other infant risks, early social risks, and concurrent social risks. Results: The results suggest that maternal negative attitude towards the infant at 6 months is an independent predictor of child behaviour problems at 5 years. This association remained significant for boys’ externalizing behaviours and girls’ internalizing behaviours. Conclusions: The findings lend support to the concept of a sensitive period in early infancy; the need for a broad perspective in the assessment of the mother-infant relationship and the need for early intervention with dysfunctional mother-infant dyads.
Identification of a Novel Rat Microsomal Vitamin D3 25-Hydroxylase*

Vitamin D3 requires the 25-hydroxylation in the liver and the subsequent 1α-hydroxylation in the kidney to exert its biological activity. Vitamin D3 25-hydroxylation is hence an essential modification step for vitamin D3 activation. Until now, three cytochrome P450 molecular species (CYP27A1, CYP2C11, and CYP2D25) have been characterized well as vitamin D3 25-hydroxylases. However, their physiological role remains unclear because of their broad substrate specificities and low activities toward vitamin D3 relative to other substrates. In this study, we purified vitamin D3 25-hydroxylase from female rat liver microsomes. The activities of the purified fraction toward vitamin D3 and 1α-hydroxyvitamin D3 were 1.1 and 13 nmol/min/nmol of P450, respectively. The purified fraction showed a few protein bands in a 50–60-kDa range on SDS-PAGE, typical for a cytochrome P450. The tryptic peptide mass fingerprinting of a protein band (56 kDa) with matrix-assisted laser desorption ionization/time of flight mass spectrometry identified this band as CYP2J3. CYP2J3 was heterologously expressed in Escherichia coli. Purified recombinant CYP2J3 showed strong 25-hydroxylation activities toward vitamin D3 and 1α-hydroxyvitamin D3 with turnover numbers of 3.3 and 22, respectively, which were markedly higher than those of P450s previously characterized as 25-hydroxylases. Quantitative PCR analysis showed that CYP2J3 mRNA is expressed at a level similar to that of CYP27A1 without marked sexual dimorphism. These results strongly suggest that CYP2J3 is the principal P450 responsible for vitamin D3 25-hydroxylation in rat liver.
Hybrid digital-analog source and channel coding with adaptation

Hybrid analog digital (HDA) architectures have been widely used in communication systems for analog source over discrete-time memoryless Gaussian channels. They employ a linear coding scheme in the analog parts, while considering separately the design of source and channel codes in the digital parts. To the best of our knowledge, none of the previous HDA schemes exploit the advantages of maintaining a joint source and channel coding design in the digital segment. In this paper, we investigate the effect of the analog parts on various outputs of the digital modules in a HDA communication system, and introduce a novel HDA architecture with adaptation for the digital parts. Such adaptation allows our system to exploit the joint effect of the analog components and the channel noise on outputs of the digital components, while simultaneously taking into consideration the unequal distribution of source code outputs. Our simulations illustrate that the proposed HDA system provides robust and graceful performance (on both bandwidth compression and expansion modes) for a wide range of channel conditions.
UnReal? Investigating the Sense of Reality and Psychotic Symptoms with Virtual Reality

Distortions of reality, such as hallucinations, are common symptoms of many psychiatric conditions. Accordingly, sense of reality (SoR), the ability to discriminate between true and false perceptions, is a central criterion in the assessment of neurological and psychiatric health. Despite the critical role of the SoR in daily life, little is known about how this is formed in the mind. Here, we propose a novel theoretical and methodological framework to study the SoR and its relation to psychotic symptoms. In two experiments, we employed a specialized immersive virtual reality (VR) environment allowing for well-controlled manipulations of visual reality. We first tested the impact of manipulating visual reality on objective perceptual thresholds (just noticeable differences). In a second experiment, we tested how these manipulations affected subjective judgments of reality. The results revealed that the objective perceptual thresholds were robust and replicable, demonstrating that SoR is a stable psychometric property that can be measured experimentally. Furthermore, reality alterations reduced subjective reality judgments across all manipulated visual aspects. Finally, reduced sensitivity to changes in visual reality was related to self-reported prodromal psychotic symptoms. These results provide evidence for the relevance of SoR in the assessment of psychosis and other mental disorders in which reality is distorted.
Progress on understanding atmospheric mercury hampered by uncertain measurements.

by Uncertain Measurements Daniel A. Jaffe,*,†,‡ Seth Lyman, Helen M. Amos, Mae S. Gustin, Jiaoyan Huang, Noelle E. Selin, Leonard Levin, Arnout ter Schure, Robert P. Mason, Robert Talbot, Andrew Rutter, Brandon Finley,† Lyatt Jaegle,‡ Viral Shah,‡ Crystal McClure,‡ Jesse Ambrose,† Lynne Gratz,† Steven Lindberg, Peter Weiss-Penzias, Guey-Rong Sheu, Dara Feddersen, Milena Horvat, Ashu Dastoor, Anthony J. Hynes, Huiting Mao, Jeroen E. Sonke, Franz Slemr, Jenny A. Fisher, Ralf Ebinghaus, Yanxu Zhang, and Grant Edwards⪫
Sol–gel processing of novel bioactive Mg-containing silicate scaffolds for alveolar bone regeneration

Periodontal tissue regeneration is an important application area of biomaterials, given the large proportion of the population affected by periodontal diseases like periodontitis. The aim of this study was the synthesis of a novel porous bioceramic scaffold in the SiO2–CaO–MgO system with specific properties targeted for alveolar bone tissue regeneration using a modification of the traditional foam replica technique. Since bioceramic scaffolds are considered brittle, scaffolds were also coated with gelatin in order to increase their mechanical stability. Gelatin was chosen for its biocompatibility, biodegradability, low-cost, and low immunogenicity. However, gelatin degrades very fast in water solutions. For this reason, two different cross-linking agents were evaluated. Genipin, a non-toxic gardenia extract and the chemical compound 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) in combination with N-hydroxysuccinimide (NHS), which is also considered non-toxic. The results of the investigation indicated that all scaffolds presented an open, interconnected porosity and pores' sizes in the range of 300–600 μm, fast apatite-forming ability, biocompatibility, and suitable mechanical stability.
Combining weak and strong mutation for a noninterpretive Java mutation system

Because of the computationally expensive cost of mutation testing, automated system support is indispensable for conducting mutation testing. Mutation systems can be classified into interpretive and noninterpretive, but recent systems are noninterpretive. Weak mutation is a well‐known cost reduction method of mutation testing, but it is not directly applicable to noninterpretive mutation systems. To address the problem and take advantage of the efficiency of weak mutation, this paper presents a combined weak and strong mutation for noninterpretive Java mutation systems. The new term ‘serialmutant’ is defined as a specialized program to conduct weak mutation against all mutants in an execution and report only weakly killed mutants as strong mutation candidates. Then strong mutation is conducted only for those reported mutants. The paper also describes an implementation based on a previous Java mutation tool, MuJava. Method‐level mutation operators for Java are also redesigned. Experimental results show that the proposed approach efficiently improves the mutation cost in a noninterpretive mutation system. Copyright © 2012 John Wiley & Sons, Ltd.