Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Logistic Model Based on Clinicopathological Features Predicts Microsatellite Instability in Colorectal Carcinomas

High-frequency microsatellite instability has been reported to be associated with good prognosis in colorectal adenocarcinoma. However, methods to assess microsatellite instability (MIN) are based on genetic assays and are not ideally suited to most histopathology laboratories. The aim of the present study was to develop a model for prediction of MIN status in colorectal cancer based on phenotypic characteristics. Clinicopathological features of a cohort of 204 patients with primary colon cancer were retrospectively reviewed following predetermined criteria. Genetic assessment of MIN status was performed on DNA extracted from sections of formalin-fixed, paraffin-embedded specimens by testing a panel of 11 microsatellite markers. Logistic regression analysis generated a mathematical tool capable of identifying colorectal tumors displaying MIN status with a sensitivity of 77.8% and a specificity of 96.8%. Features associated with instability included the proximal location of the lesions, occurrence of solid and/or mucinous differentiation, absence of cribriform structures, presence of peritumoral Crohn-like reaction, expansive growth pattern, high Ki67 proliferative index, and p53-negative phenotype. This approach predicts microsatellite instability in colorectal carcinoma with an overall assigned accuracy of 95.1% and a negative predictive value of 97.8%. Implementation of this tool to routine histopathological studies could improve the management of patients with colorectal cancer, especially those presenting with stage II and III of the disease. It will also assist in identifying a subset of patients likely to benefit from adjuvant chemotherapy.
Comparative effects of in ovo versus subcutaneous administration of the Marek's disease vaccine and pre-placement holding time on the processing yield of Ross 708 broilers1,2,3

ABSTRACT Effects of the in ovo (i.o.) or subcutaneous (s.c.) method of administration (moa) of the Marek's disease (MD) vaccine and 4 or 18 h pre‐placement holding time (pht) on the processing yield of male broilers through 49 d of age (doa) were investigated. Ross 708 broiler hatching eggs (3,900) were either i.o. ‐vaccinated at 18 d of incubation or chicks from eggs that were not i.o. ‐vaccinated were s.c. ‐vaccinated at hatch. The i.o. injections (50 &mgr;L) were delivered by a commercial multi‐egg injector and s.c. injections (200 &mgr;L) were delivered by an automatic pneumatic s.c. injector. The pht was imposed on chicks after vaccination. Sixteen birds were initially assigned to each of 15 replicate floor pens belonging to each of the moa and pht combination groups and were grown out through 48 doa. At 48 doa, 6 birds were randomly selected from each replicate pen and were weighed and fasted for 16 h before being processed. At 49 doa, whole carcass, fat pad, breast muscle, and tenders muscles weights were recorded. Whole carcass weight as a percentage of live BW, and fat pad, breast muscle, and tenders muscles weights as percentages of both live and whole carcass weights were calculated. Upon subjection of the data to a 2 × 2 factorial analysis, only a main effect due to moa was observed for tenders muscles weight as a percentage of live and whole carcass weights. Tenders muscles weight as a percentage of both live (P ≤ 0.010) and whole carcass (P ≤ 0.004) weight was higher in birds hatched from eggs that received i.o. rather than s.c. vaccinations. In conclusion, in comparison to s.c. vaccination, i.o. vaccination increased relative tenders weight yield, whether or not broilers were held for 4 or 18 h prior to placement. Therefore, with regard to broiler processing yield, i.o. and s.c. vaccinations were safe for the administration of the MD vaccine, with i.o. vaccination displaying a slight potential advantage.
Dysrhythmia of Caloric Nystagmus

Objectives Objectives of the study were 1) to determine the prevalence and characteristics of dysrhythmia, 2) to identify associations between dysrhythmia and other patient variables, and 3) to determine whether dysrhythmia is more a characteristic of individuals than simply a correlate of alertness or response intensity.
Testing Models of Media Performance in Wartime: U.K. TV News and the 2003 Invasion of Iraq

Debate over media coverage of foreign affairs has been dominated by a range of theoretical positions, here characterized as the `elite-driven,' 'independent' and 'oppositional' models. In this article, we explore the relative cogency of these theoretical positions in the context of British media coverage of the 2003 Iraq War. We find that coverage generally conformed to the elite-driven model, reinforcing the coalition. Nevertheless, our analysis also provides evidence to support the independent and oppositional models. Regarding casualties and the humanitarian situation, we find significant levels of coverage which support the oppositional model and the notion of event-driven news. Overall, our study points toward a more nuanced understanding of media-state relations than is suggested by the existing elite-driven paradigm.
Eating‐disordered patients with and without self‐injurious behaviours: a comparison of psychopathological features

Objective: A considerable number of eating-disordered patients also display all kinds of self-injurious behaviours (SIB), which might be viewed as an indicator of psychopathological severity. Method: To test this hypothesis in 70 females admitted to a specialized treatment programme for eating disorders, a wide spectrum of psychopathological features was studied by means of self-reporting questionnaires: clinical symptomatology, personality disorders, aggression regulation, trauma history, dissociation and body experience. A comparison was made between patients with (n = 27) and without SIB (n = 43), as well as between patients with one (n = 13) versus more types (n = 14) of SIB. Results: In general, patients with SIB reported significantly more complaints or signs of anxiety, depression, hostility, cluster B personality disorders, feelings of anger, traumatic experiences, dissociation and negative appreciation of body size. The presence of more than one type of SIB was linked to a more pronounced clinical symptomatology and trauma history. Copyright © 2003 John Wiley & Sons, Ltd and Eating Disorders Association.
Frequency-domain Channel Frequency Response Estimation for Space-Time Coded MIMO Systems

Frequency-domain equalization (FDE) is an effective technique to mitigate the distortion induced by long-spanning inter-symbol interference, but the receiver requires to estimate the channel information. In this paper, we present a training-based frequency-domain channel frequency response (CFR) estimation scheme, which is hardware efficient when integrating with FDE for space-time (ST) coded multiple-input multiple-output (MIMO) transmissions over frequency-selective fading channels. In this proposed scheme, training sequences are ST block encoded at the transmitter. Similar to when performing FDE, the training sequences are processed after the FFT operation to obtain the CFR. A thorough analysis of the CFR estimation mean square error (MSE) is provided based on both the least squares (LS) and minimum MSE (MMSE) criteria, with the transmit power constraint and the optimal choices of training signals being taken into account. Finally, we demonstrate that when the number of transmit antennas is equal to 2, this CFR estimation could be implemented recursively by means of certain adaptive algorithms. Simulation results are presented to demonstrate the effectiveness of our proposed scheme in joint with FDE in multipath fading channels.
Polyploidy road to therapy‐induced cellular senescence and escape

Therapy‐induced cellular senescence (TCS), characterized by prolonged cell cycle arrest, is an in vivo response of human cancers to chemotherapy and radiation. Unfortunately, TCS is reversible for a subset of senescent cells, leading to cellular reproliferation and ultimately tumor progression. This invariable consequence of TCS recapitulates the clinical treatment experience of patients with advanced cancer. We report the findings of a clinicopathological study in patients with locally advanced non‐small cell lung cancer demonstrating that marker of in vivo TCS following neoadjuvant therapy prognosticate adverse clinical outcome. In our efforts to elucidate key molecular pathways underlying TCS and cell cycle escape, we have previously shown that the deregulation of mitotic kinase Cdk1 and its downstream effectors are important mediators of survival and cell cycle reentry. We now report that aberrant expression of Cdk1 interferes with apoptosis and promotes the formation of polyploid senescent cells during TCS. These polyploid senescent cells represent important transition states through which escape preferentially occurs. The Cdk1 pathway is in part modulated differentially by p21 and p27 two members of the KIP cyclin‐dependent kinase inhibitor family during TCS. Altogether, these studies underscore the importance of TCS in cancer therapeutics.
Leukocyte telomeres are longer in African Americans than in whites: the National Heart, Lung, and Blood Institute Family Heart Study and the Bogalusa Heart Study

Leukocyte telomere length (LTL) is ostensibly a bio‐indicator of human aging. Here we report that African Americans have longer LTL than whites. We studied cross‐sectionally 2453 individuals from the National Heart, Lung, and Blood Institute (NHLBI) Family Heart Study (age = 30–93 years) and the Bogalusa Heart Study (age = 19–37 years), comprising 1742 whites and 711 African Americans. We measured LTL by Southern blots of the terminal restriction fragments length. In 234 participants, telomere repeats were also measured by quantitative polymerase chain reaction (qPCR). Adjusted for age and body mass index (BMI), the respective leukocyte telomere lengths (mean ± SEM) were considerably longer in African Americans than in whites both in the Family Heart Study (7.004 ± 0.033 kb vs. 6.735 ± 0.024 kb, p < 0.0001) and the Bogalusa Heart Study (7.923 ± 0.063 kb vs. 7.296 ± 0.039 kb, p < 0.0001). We confirmed the racial effect on LTL by qPCR (3.038 ± 0.565 T/S units for African Americans vs. 2.714 ± 0.487 T/S units for whites, p < 0.001). Cross‐sectionally, sex‐ and BMI‐adjusted LTL became shorter with age (range 19–93 years) at a steeper slope in African Americans than in whites (0.029 kb year−1 vs. 0.020 kb year−1, respectively, p = 0.0001). We suggest that racial difference in LTL arises from a host of interacting biological factors, including replication rates of hematopoietic stem cells.
Engineering of Bispecific Affinity Proteins with High Affinity for ERBB2 and Adaptable Binding to Albumin

The epidermal growth factor receptor 2, ERBB2, is a well-validated target for cancer diagnostics and therapy. Recent studies suggest that the over-expression of this receptor in various cancers might also be exploited for antibody-based payload delivery, e.g. antibody drug conjugates. In such strategies, the full-length antibody format is probably not required for therapeutic effect and smaller tumor-specific affinity proteins might be an alternative. However, small proteins and peptides generally suffer from fast excretion through the kidneys, and thereby require frequent administration in order to maintain a therapeutic concentration. In an attempt aimed at combining ERBB2-targeting with antibody-like pharmacokinetic properties in a small protein format, we have engineered bispecific ERBB2-binding proteins that are based on a small albumin-binding domain. Phage display selection against ERBB2 was used for identification of a lead candidate, followed by affinity maturation using second-generation libraries. Cell surface display and flow-cytometric sorting allowed stringent selection of top candidates from pools pre-enriched by phage display. Several affinity-matured molecules were shown to bind human ERBB2 with sub-nanomolar affinity while retaining the interaction with human serum albumin. Moreover, parallel selections against ERBB2 in the presence of human serum albumin identified several amino acid substitutions that dramatically modulate the albumin affinity, which could provide a convenient means to control the pharmacokinetics. The new affinity proteins competed for ERBB2-binding with the monoclonal antibody trastuzumab and recognized the native receptor on a human cancer cell line. Hence, high affinity tumor targeting and tunable albumin binding were combined in one small adaptable protein.
Predacious activity of Ants (Hymenoptera: Formicidae) in conventional and in No-till agriculture systems

This study had the objective of assessing the differences in foraging activity of the predacious ants between two areas, one conventional and other with no-till agriculture systems. The research was conducted in two contiguous 1.5 ha plots in Dourados MS, Brazil, from February 2001 to December 2003. Each plot received 750 baits (Nasutitermes termites), 425 at daylight and 325 at night. The termites were placed on the filter paper, on the ground, and ant attack was monitored for 15 min, until removed. Sixteen ant species were found in the no-till system and nine in the conventional system. Baits removed from no-till were significantly higher than the conventional plots and were influenced by the sampling time, at day or night. The seasons of the year did not significantly explain the variations in the structure of the predacious ant communities in neither of the systems. The significant differences at foraging activity and ant richness between the areas indicated that the no-tillage system could improve environmental quality of the cropping and therefore, became an important tool for the integrated pest management programs.
Social Context and Video Game Play: Impact on Cardiovascular and Affective Responses

We examined if cardiovascular and affective responding to video game play changed across social context or with game content. Male participants (13–22 years old) played a violent or nonviolent video game. Each participant played the game individually, competitively against a male partner, and cooperatively with the partner. There was no effect of social condition on heart rate (HR) or diastolic blood pressure (DBP). Participants had significantly higher systolic BP (SBP) when playing individually and competitively than when playing cooperatively, probably because play was more continuous. There was no impact of game type for HR or SBP. DBP was significantly higher for participants who played the violent game, perhaps because participants found the violent game more exciting and enjoyable. Participants who played the violent game rated the experimenters more positively than those who played the nonviolent game. Participants found game play more exciting, enjoyable, stressful, and frustrating, but less boring and relaxing, when they played competitively or cooperatively than when they played individually. The results are discussed in terms of the general aggression model.
Adaptive Extents-Based File System for Object-Based Storage Devices

Object-Based Storage Systems is emerging as the storage architecture in the next wave of storage technology. An Object-Based Storage System is rquired to deal with objectbased storage devices (OSD) workloads which are generally different from the general purpose file system workloads. This paper describe how we implemented a userlevel Object-Based Storage Device File System (OSDFS) which utilizes extents in the traditional bitmap, an adaptive metadata updating scheme, a wasted free space data allocation scheme, extended size of an object mapping (onode ID) to include information of metadata so as to achieve a high performance and high throughput file system for OSD. Our experiments show that OSDFS is able to maintain its continuity in allocating free space for objects up to 98% of disk utilization. In addition, OSDFS is not only outperforms ext2 and ext3 in handling OSD workloads , but also provides better performance when dealing with general purpose file system workloads a compared to conventional file systems.
Contribution of the KCa3.1 channel–calmodulin interactions to the regulation of the KCa3.1 gating process

The Ca2+-activated potassium channel of intermediate conductance, KCa3.1, is now emerging as a therapeutic target for a large variety of health disorders. The Ca2+ sensitivity of KCa3.1 is conferred by the Ca2+-binding protein calmodulin (CaM), with the CaM C-lobe constitutively bound to an intracellular domain of the channel C terminus. It was proposed on the basis of the crystal structure obtained for the C-terminal region of the rat KCa2.2 channel (rSK2) with CaM that the binding of Ca2+ to the CaM N-lobe results in CaM interlocking the C-terminal regions of two adjacent KCa3.1 subunits, leading to the formation of a dimeric structure. A study was thus undertaken to identify residues of the CaM N-lobe–KCa3.1 complex that either contribute to the channel activation process or control the channel open probability at saturating Ca2+ (Pomax). A structural homology model of the KCa3.1–CaM complex was first generated using as template the crystal structure of the C-terminal region of the rat KCa2.2 channel with CaM. This model was confirmed by cross-bridging residues R362 of KCa3.1 and K75 of CaM. Patch-clamp experiments were next performed, demonstrating that the solvation energy of the residue at position 367 in KCa3.1 is a key determinant to the channel Pomax and deactivation time toff. Mutations of residues M368 and Q364 predicted to form anchoring points for CaM binding to KCa3.1 had little impact on either toff or Pomax. Finally, our results show that channel activation depends on electrostatic interactions involving the charged residues R362 and E363, added to a nonpolar energy contribution coming from M368. We conclude that electrostatic interactions involving residues R362 and E363 and hydrophobic effects at M368 play a prominent role in KCa3.1 activation, whereas hydrophobic interactions at S367 are determinant to the stability of the CaM–KCa3.1 complex throughout gating.
Listeriolysin S, a Novel Peptide Haemolysin Associated with a Subset of Lineage I Listeria monocytogenes

Streptolysin S (SLS) is a bacteriocin-like haemolytic and cytotoxic virulence factor that plays a key role in the virulence of Group A Streptococcus (GAS), the causative agent of pharyngitis, impetigo, necrotizing fasciitis and streptococcal toxic shock syndrome. Although it has long been thought that SLS and related peptides are produced by GAS and related streptococci only, there is evidence to suggest that a number of the most notorious Gram-positive pathogenic bacteria, including Listeria monocytogenes, Clostridium botulinum and Staphylococcus aureus, produce related peptides. The distribution of the L. monocytogenes cluster is particularly noteworthy in that it is found exclusively among a subset of lineage I strains; i.e., those responsible for the majority of outbreaks of listeriosis. Expression of these genes results in the production of a haemolytic and cytotoxic factor, designated Listeriolysin S, which contributes to virulence of the pathogen as assessed by murine- and human polymorphonuclear neutrophil–based studies. Thus, in the process of establishing the existence of an extended family of SLS-like modified virulence peptides (MVPs), the genetic basis for the enhanced virulence of a proportion of lineage I L. monocytogenes may have been revealed.
Faculty Helpfulness to Students

A total of 154 randomly chosen faculty members at a large public university served as subjects in a study of compliance by professors to students' request for help. The door-in-the-face technique (large initial request, followed by a moderate request) elicited significantly more compliance than the foot-in-the-door technique (small initial request, followed by a moderate request) and the control technique (moderate request only). The foot-in-the-door technique was significantly less effective than the control technique. The results were viewed conceptually and pragmatically.
Cloning and Characterization of the xyl1 Gene, Encoding an NADH-Preferring Xylose Reductase from Candida parapsilosis, and Its Functional Expression in Candida tropicalis

ABSTRACT Xylose reductase (XR) is a key enzyme in d-xylose metabolism, catalyzing the reduction of d-xylose to xylitol. An NADH-preferring XR was purified to homogeneity from Candida parapsilosis KFCC-10875, and the xyl1 gene encoding a 324-amino-acid polypeptide with a molecular mass of 36,629 Da was subsequently isolated using internal amino acid sequences and 5′ and 3′ rapid amplification of cDNA ends. The C. parapsilosis XR showed high catalytic efficiency (kcat/Km = 1.46 s−1 mM−1) for d-xylose and showed unusual coenzyme specificity, with greater catalytic efficiency with NADH (kcat/Km = 1.39 × 104 s−1 mM−1) than with NADPH (kcat/Km = 1.27 × 102 s−1 mM−1), unlike all other aldose reductases characterized. Studies of initial velocity and product inhibition suggest that the reaction proceeds via a sequentially ordered Bi Bi mechanism, which is typical of XRs. Candida tropicalis KFCC-10960 has been reported to have the highest xylitol production yield and rate. It has been suggested, however, that NADPH-dependent XRs, including the XR of C. tropicalis, are limited by the coenzyme availability and thus limit the production of xylitol. The C. parapsilosis xyl1 gene was placed under the control of an alcohol dehydrogenase promoter and integrated into the genome of C. tropicalis. The resulting recombinant yeast, C. tropicalis BN-1, showed higher yield and productivity (by 5 and 25%, respectively) than the wild strain and lower production of by-products, thus facilitating the purification process. The XRs partially purified from C. tropicalis BN-1 exhibited dual coenzyme specificity for both NADH and NADPH, indicating the functional expression of the C. parapsilosis xyl1 gene in C. tropicalis BN-1. This is the first report of the cloning of an xyl1 gene encoding an NADH-preferring XR and its functional expression in C. tropicalis, a yeast currently used for industrial production of xylitol.
The transition to automated practitioner order entry in a teaching hospital: the VA Puget Sound experience

We recently installed an automated practitioner order entry system on our busiest inpatient wards and critical care units. The installation followed 20 months preparation in which we created the workstation, network, and host infrastructure, developed requisite policies, recruited personnel to support the system, and installed the software in areas where the pace of order entry was less intense. Since implementing automated order entry, we have experienced problems such as an increase in time required for practitioners to enter orders, workflow changes on inpatient units, difficulties with patient transfers, and others. Our user support system has been heavily used during the transition period. Software tailoring and enhancements designed to address these problems are planned, as is installation of the order entry system in remaining clinical units in our medical centers.
Quasi-static scheduling for real-time systems with hard and soft tasks

This paper addresses the problem of scheduling for real-time systems that include both hard and soft tasks. The relative importance of soft tasks and how the quality of results is affected when missing a soft deadline are captured by utility functions associated to soft tasks. Thus the aim is to find the execution order of tasks that makes the total utility maximum and guarantees hard deadlines. We consider time intervals rather than fixed execution times for tasks. Since a purely off-line solution is too pessimistic and a purely on-line approach incurs an unacceptable overhead due to the high complexity of the problem, we propose a quasi-static approach where a number of schedules are prepared at design-time and the decision of which of them to follow is taken at run-time based on the actual execution times. We propose an exact algorithm as well as different heuristics for the problem addressed in this paper.