Miracle-dz/UniFAR-FTUs huggingface dataset:
The Advantage of Discordance: An Example Using the Highly Subjective Nuclear Grading of Breast Cancer

Discordance among multiple assessments has been a reason to criticize a biomarker. But, if different assessments are all relevant, the meaning of discordance requires explanation. As an example, for 1085 breast cancers, a low (score 1), intermediate (score 2) or high nuclear grade (NG) (score 3) was assigned in years 2013, 2015, 2016. Year apart readings allowed for memory lapse of prior readings. For each cancer, scores for NG2013, NG2015, NG2016 were added together to yield sum score nuclear grade (SSNG) with range 3 to 9. SSNG was used to find if discrepancy between NG readings carried information for patient outcome. Discrepancies were inherent with SSNG=4, 5, 7 or 8. Time-dependent receiver operator curves were central for evaluating discordance as related to patient outcome. Area under curves for SSNG, and the component NGs, in stage 1, stage 2, and stage 3 cancers were, respectively: SSNG: 70, 68, 75; NG2013: 70, 63, 71; NG2015: 67, 65, 74; and NG2016: 65, 66, 68. The area under curves of SSNG was not significantly lower than any of the components from which it was derived. This is despite discordant readings having been incorporated into SSNG. Among the 3 readings, 50.1% were discordant, yet only 2.1% were low/high discrepancy. Concordance in high-grade assignment (SSNG=9) corresponded to poor prognosis. If morphologic features are midway between 2 predefined levels it is sensible that separate readings will be distributed between adjacent levels. Shown has been how an “in-between” level helps predict survival then discordance discovery offers classification. Discordance discovery can conceivably be embraced for real-world applications.
Molecular cloning and characterization of the genes (pbpA and rodA) responsible for the rod shape of Escherichia coli K-12: analysis of gene expression with transposon Tn5 mutagenesis and protein synthesis directed by constructed plasmids

Two cell shape-determining genes of Escherichia coli K-12, pbpA, the structural gene for penicillin-binding protein 2, and rodA, whose protein is unknown, were subcloned into plasmid vectors from the transducing phage lambda MAd lip24, which carries the lip-leuS region of the E. coli chromosome. Plasmids with restriction enzyme-created deletions or transposon Tn5 insertions were isolated, and studies of genetic complementation of these plasmids with chromosomal mutations were carried out. Thus, a physical and genetic map of the rodA-pbpA region was established. The genes rodA and pbpA lie side by side within a 4.4-kilobase-pair region. The size of the rodA gene has been shown to be between 0.86 and 1.6 kilobase pairs; such DNA would encode a protein with a molecular weight between 32,000 and 59,000. Since Tn5 mutagenesis of the rodA gene did not affect the expression of the pbpA gene and vice versa, the genes rodA and pbpA seem to have independent promoters. Analysis of the proteins synthesized from the constructed plasmids in maxicells revealed that the plasmid carrying the pbpA gene encoded penicillin-binding protein 2 and amplification of the protein occurred. The product of the rodA gene was not identified.
Improving UAV Traffic Management using Fog Computing

The System-Wide Information Management (SWIM) is a program destined to manage every aspect of aviation traffic in the near future, but given the system's enormous amount of information, and the rise of Unmanned Aerial Vehicles (UAV), the system is bound to run into problems. The introduction of the Internet of Things (IoT) solutions, such as fog computing, could allow for a more secure and distributed management UAVs traffic management as part of the National Airspace, as well as to solve the System-Wide Information Management potential future shortcomings. This paper seeks to introduce an approach to integrate the concept of fog computing and the SWIM architecture in order to provide an improved and more reliable solution to airport traffic management in and around Tower and TRACON facilities, where there is a chance of intrusion by small Unmanned Aerial Vehicles.
Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes

Pathogens in the genus Campylobacter are the most common cause of food-borne bacterial gastro-enteritis. Campylobacteriosis, caused principally by Campylobacter jejuni and Campylobacter coli, is transmitted to humans by food of animal origin, especially poultry. As for many pathogens, antimicrobial resistance in Campylobacter is increasing at an alarming rate. Erythromycin prescription is the treatment of choice for clinical cases requiring antimicrobial therapy but this is compromised by mobility of the erythromycin resistance gene erm(B) between strains. Here, we evaluate resistance to six antimicrobials in 170 Campylobacter isolates (133 C. coli and 37 C. jejuni) from turkeys. Erythromycin resistant isolates (n = 85; 81 C. coli and 4 C. jejuni) were screened for the presence of the erm(B) gene, that has not previously been identified in isolates from turkeys. The genomes of two positive C. coli isolates were sequenced and in both isolates the erm(B) gene clustered with resistance determinants against aminoglycosides plus tetracycline, including aad9, aadE, aph(2″)-IIIa, aph(3′)-IIIa, and tet(O) genes. Comparative genomic analysis identified identical erm(B) sequences among Campylobacter from turkeys, Streptococcus suis from pigs and Enterococcus faecium and Clostridium difficile from humans. This is consistent with multiple horizontal transfer events among different bacterial species colonizing turkeys. This example highlights the potential for dissemination of antimicrobial resistance across bacterial species boundaries which may compromise their effectiveness in antimicrobial therapy.
Effect of intraperitoneal or incisional bupivacaine on pain and the analgesic requirement after ovariohysterectomy in dogs.

OBJECTIVE To compare the effect of intraperitoneal (IP) or incisional (INC) bupivacaine on pain and the analgesic requirement after ovariohysterectomy in dogs. STUDY DESIGN Prospective, randomized clinical study. ANIMALS Thirty female dogs undergoing ovariohysterectomy (OHE). METHODS Dogs admitted for elective OHE were anesthetized with acepromazine, butorphanol, thiopental and halothane. Animals were randomly assigned to one of three groups (n = 10 per group). The treatments consisted of preincisional infiltration with saline solution (NaCl 0.9%) or bupivacaine with epinephrine and/or IP administration of the same solutions, as follows: INC and IP 0.9% NaCl (control group); INC 0.9% NaCl and IP bupivacaine (5 mg kg(-1), IP group); INC bupivacaine (1 mg kg(-1)) and IP 0.9% NaCl (INC group). Postoperative pain was evaluated by a blinded observer for 24 hours after extubation by means of a visual analog scale (VAS) and a numeric rating scale (NRS). Rescue analgesia (morphine, 0.5 mg kg(-1) , IM) was administered if the VAS was >5/10 or the NRS >10/29. RESULTS At 1 hour after anesthesia, VAS pain scores were [medians (interquartile range)]: 6.4 (3.1-7.9), 0.3 (0.0-2.6) and 0.0 (0.0-7.0) in control, IP and INC groups, respectively. VAS pain scores were lower in the IP compared to the control group. Over the first 24 hours, rescue analgesia was administered to 7/10, 5/10 and 3/10 dogs of the control, INC and IP groups, respectively. Total number of dogs given rescue analgesia over the first 24 hours did not differ significantly among groups. CONCLUSIONS AND CLINICAL RELEVANCE Intraperitoneal bupivacaine resulted in lower pain scores during the first hour of the postoperative period and there was a trend towards a decreased need for rescue analgesia after OHE in dogs.
The Problem of Abortion and the Doctrine of the Double Effect

One of the reasons why most of us feel puzzled about the problem of abortion is that we want, and do not want, to allow to the unborn child the rights that belong to adults and children. When we think of a baby about to be born it seems absurd to think that the next few minutes or even hours could make so radical a difference to its status; yet as we go back in the life of the foetus we are more and more reluctant to say that this is a human being and must be treated as such. No doubt this is the deepest source of our dilemma, but it is not the only one. For we are also confused about the general question of what we may and may not do where the interests of human beings conflict. We have strong intuitions about certain cases; saying, for instance, that it is all right to raise the level of education in our country, though statistics allow us to predict that a rise in the suicide rate will follow, while it is not all right to kill the feeble-minded to aid cancer research. It is not easy, however, to see the principles involved, and one way of throwing light on the abortion issue will be by setting up parallels involving adults or children once born. So we will be able to isolate the ‘equal rights’ issue and should be able to make some advance.
Theoretical cost effectiveness of management options for children with persisting middle ear effusions.

OBJECTIVE The purpose of this theoretical study is to assess the cost effectiveness of options involving observation, antibiotics alone, corticosteroids alone, corticosteroids plus antibiotics, and surgery to clear persisting middle ear effusions during three visits. METHODOLOGY In a hypothetical case the expected average per patient expenditures are calculated using the efficacy rates determined by the meta-analysis of randomized controlled clinical trials involving corticosteroids plus an antibiotic (six trials), corticosteroids alone (three trials), and antibiotic alone (four trials). In this analysis, all children whose bilateral middle ear effusions persist for 12 weeks despite medical management are referred for ventilating tubes. RESULTS The most cost-effective intervention combination is corticosteroid plus an antibiotic at visit 1 (6 weeks after diagnosis of acute otitis media) followed by a second antibiotic in nonresponders at visit 2 (9 weeks after diagnosis of acute otitis media) and referral for ventilating tubes in nonresponders at visit 3 (12 weeks after diagnosis of acute otitis media). The expected average expenditures per case to clear the bilateral middle ear effusions is $600.91 based on reimbursement of private practice charges and $350.27 based on Medicaid reimbursement (all payments to providers are based on 1992 data from Colorado). The difference in the expected average total expenditures per case between this most cost-effective approach versus the use of sequential courses of antibiotics followed by surgery is $372.81 ($973.72-$600.91) with full reimbursement of private practice charges and $202.57 ($552.84-$350.27) with Medicaid reimbursement. In clearing the middle ear effusion, the average estimated travel expenses per case is $21.46, and lost parental wages per case are $45.12. When the expenditures associated with an additional 6-month follow-up period are included, the expected average per case expenditures is $1088.54 with reimbursement of private practice charges and @659.00 with Medicaid reimbursement. The difference in the expected average per case expenditures to clear the effusions and follow-up for 6 months between the most cost-effective approach using corticosteroids plus antibiotics at the 6- and 9-week visits followed by surgery in nonresponders at 12 weeks versus sequential courses of antibiotics is $405.30 ($1493.84-$1088.54) with reimbursement of private practice charges and $217.32 ($876.32-$659.00) with Medicaid reimbursement. RECOMMENDATIONS Although the analysis does not consider risks, side effects, and parental or provider preferences, the findings suggest that the implementation of cost-effective clinical guidelines can potentially reduce national expenditures for managing persistent middle ear effusions.
MagCAD: Tool for the Design of 3-D Magnetic Circuits

The post-CMOS scenario poses many challenges to researchers. Innovative solutions must be found to further improve electronic circuits. Exploiting the potential offered by the third dimension is clearly one of the best possibilities available. However, due to the lack of a simple and straightforward methodology, it is difficult to analyze and compare beyond-CMOS technologies. We tackle this challenge by presenting a framework that enables the design of 3-D circuits based on field-coupled technologies. The tool is called MagCAD and is part of the ToPoliNano design suite, created to design and simulate circuits based on emerging technologies by applying a top–down methodology. Right now, MagCAD supports the two main implementations of nanomagnetic logic (NML), the in-plane NML, and the perpendicular NML (pNML). However, it is designed to be easily extended to other beyond-CMOS technologies. Researchers can design pNML circuits by using MagCAD, which embeds design rules, physical models, and technological parameters. The compact model and the physical properties of these cells are based on experimental results. After the design phase, a register-transfer-level model of the circuit is automatically extracted by MagCAD. The model is written in VHSIC Hardware Description Language and has been validated through experiments. The extracted model can be simulated with fast HDL-simulators; this makes it possible to verify the behavior and extract the performance of the designed circuit. With MagCAD, designers have the possibility to easily design, simulate, and compare 3-D NML circuits, exploring the advantages provided by the third dimension freely.
Binding of a murine proteinase inhibitor to the acrosome region of the human sperm head

Proteinase inhibitors are present in the various glands, tissues, and secretions of the male reproductive tract. Some of these inhibitors bind to the acrosomal region of the sperm, and their release during in vitro or in utero incubation suggests that they may play a role in capacitation. In the mouse, the binding site for a trypsin‐acrosin inhibitor, the acceptor, has been implicated in capacitation, zona binding, and the acrosome reaction. This presentation demonstrates that a component, molecular weight ˜T20,000, on the human sperm head may recognize the murine inhibitor. Furthermore, the acrosome reaction can be induced in capacitated human sperm by immunoaggregation of bound murine inhibitor. The data indicate that the proteinase inhibitor binding site on the human sperm head may, as with a similar site on murine sperm, play a role in the early events of fertilization. © 1993 Wiley‐Liss, Inc.
Effects of static stretching on the maximal length and resistance to passive stretch of short hamstring muscles.

This project was supported in part by a grant from The Foundation for Physical Therapy, 1111 North Fairfax Street, Alexandria, VA 22314 Foreshortened hamstring muscles have been associated with various clinical disorders. This study examined the effects of three weeks of daily static stretching of short hamstrings on passive straight leg raising (SLR), maximal hamstring length (MHL), and their maximal resistance to passive stretch (MRPS). Twenty-four healthy men (18-37 yrs) with SLR </= 70 degrees were assigned randomly to a stretching group (N = 12) or a control group (N = 12). All subjects were positioned on their left sides with the pelvis stabilized and the right thigh fixed at 90 degrees on a horizontal platform. The right knee was then passively extended until amplified EMG activity (>50 muV) from the hamstrings was observed. The knee angle represented MHL, and MRPS (torque in nm) was calculated. Subjects in the stretching group completed daily static stretching of the hamstrings for three weeks. After three weeks, SIR increased for the stretching group, but not for the control group (< 0.001). The knee angle for the stretching group was less than the control group (p < 0.001), and the MRPS for the stretching group exceeded the control group (p < 0.05). The results indicated that static stretching increased SLR with concomitant increases in the MHL and the MRPS. The results also support using SLR as a valid clinical test for measuring hamstring length changes resulting from therapeutic interventions. J Orthop Sports Phys Ther 1991;14(6):250-255.
Temporo‐frontal Disconnection Impairs Visual‐visual Paired Association Learning but not Configural Learning in Macaca Monkeys

Cynomolgus monkeys were tested in two computer‐controlled visual associative memory tasks. The monkeys chose between visual objects on a screen by touching one. In the configural learning task one correct object and one wrong object were presented in each trial. Each of these two objects was composed of two coloured alphanumeric characters abutted together. The designation of the objects as ‘correct’ or ‘wrong’ followed a configural rule: e.g. if AB and CD are correct objects then AD and CB are wrong. In the paired association learning task in each trial three spatially separate objects (single alphanumeric characters) were presented. The central object was an instruction cue and the designation of the side objects as ‘correct’ or ‘wrong’ choices followed a paired association rule: e.g. if A, C and B are presented (C in the centre) then A is correct and B is wrong: however, if A, D and C are presented then C is correct and A is wrong. Disrupting the direct cortico‐cortical interaction between the inferior temporal cortex and the prefrontal cortex by uncinate fascicle transection led to a learning deficit in the paired association task but not in the configural task. These results suggest that the uncinate fascicle facilitates visual‐visual associative learning only in the specific case where a visual object acts as an instruction cue to guide the conditional choice of another, spatially separate object, and they support the evidence for a specific role of the uncinate fascicle in the learning of conditional tasks with visual instruction cues.
Is 24-hour Intraocular Pressure Monitoring Necessary in Glaucoma?

Abstract Although intraocular pressure (IOP) is the only treatable risk factor for glaucoma, its 24-hour behavior is poorly understood. Conflicting information is available in the literature with regard to the importance and predictive value of IOP peaks and fluctuations on the risk of glaucoma development and progression. This may be secondary to lack of prospective studies designed to address this issue. This article critically reviews the current evidence for the importance of 24-h IOP measurements in glaucoma and discusses shortcomings of current methods to assess 24-h IOP data, drawing attention to new developments in this field.
The holy grail of metabolic disease: brown adipose tissue

Purpose of review The finding that brown adipose tissue (BAT) is present in adults brought BAT physiology into the focus of many researchers interested in energy metabolism. Here, we review recent insight into how BAT develops, functions and might help to treat metabolic disorders in humans. Recent findings BAT is under control of the nervous system, and several pathways have been identified that allow direct manipulation of BAT biology. In addition, some brown adipocytes arise from a distinct subset of white adipocyte precursors and studies were performed that characterize the development of these ‘brite’ adipocytes. Importantly, progress has been made in understanding how BAT takes up and dissipates nutrients that in metabolic disorders are present in excess. Finally, as it seems that BAT activity declines with age and obesity, we review findings that might shed light on how humans could sustain or increase BAT activity, thus preventing or treating obesity, hyperlipidemia and type 2 diabetes. Summary BAT is a powerful organ that controls the development of metabolic disease. These powers are boosted by mechanisms that turn white into brown fat and enhance lipid flux into BAT. However, in humans, it remains unclear what was the first: metabolic disease or decreased BAT activity.
Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant Escherichia coli

Relative levels of many individual proteins in Escherichia coli HB101 strains with 0, 37, 56, and 240 plasmids per chromosome were determined by computer image analysis of two‐dimensional gel electrophoresis patterns. The plasmids investigated had very similar sequences except for small domains encoding the represser of plasmid replication. At the intermediate plasmid copy number of 56, levels of several of the TCA cycle enzymes (oxoglutarate dehydrogenase complex, succinate thiokinase, and succinate dehydrogenase) as well as in aspartate transcarbamoylase increased. At a plasmid copy number of 240, higher amounts of PEP carboxylase as well as several of the heat shock proteins were observed. Furthermore, at high plasmid levels, significant decreases occurred in growth rate, pyruvate kinase I, pyruvate dehydrogenase complex, unadenylated glutamine synthetase, aspartate transcarbamoylase as well as in several of the proteins involved in translation. Decreases in ribosome content as well as in the free 30S and 50S ribosomal subunit pool fractions were also observed in separate analyses. These results indicate that recombinant DNA manipulations can cause major alterations in numerous host cell properties which could significantly influence cloned protein production or metabolic engineering endeavors.
Nucleolin binds specifically to an AP‐1 DNA sequence and represses AP1‐dependent transactivation of the matrix metalloproteinase‐13 gene

Transcriptional regulation via activator protein‐1 (AP‐1) protein binding to AP‐1 binding sites within gene promoter regions of AP‐1 target genes plays a key role in controlling cellular invasion, proliferation, and oncogenesis, and is important to pathogenesis of arthritis and cardiovascular disease. To identify new proteins that interact with the AP‐1 DNA binding site, we performed the DNA affinity chromatography‐based Nucleotide Affinity Preincubation Specificity TEst of Recognition (NAPSTER) assay, and discovered a 97 kDa protein that binds in vitro to a minimal AP‐1 DNA sequence element. Mass spectrometric fragmentation sequencing determined that p97 is nucleolin. Immunoblotting of DNA affinity‐purified material with anti‐nucleolin antibodies confirmed this identification. Nucleolin also binds the AP‐1 site in gel shift assays. Nucleolin interacts in NAPSTER with the AP‐1 site within the promoter sequence of the metalloproteinase‐13 gene (MMP‐13), and binds in vivo in chromatin immunoprecipitation assays in the vicinity of the AP‐1 site in the MMP‐13 promoter. Overexpression of nucleolin in human HeLa cervical carcinoma cells significantly represses AP‐1 dependent gene transactivation of a minimal AP‐1 reporter construct and of an MMP‐13 promoter reporter sequence. This is the first report of nucleolin binding and transregulation at the AP‐1 site. © 2007 Wiley‐Liss, Inc.