Miracle-dz/UniFAR-FTUs huggingface dataset:
Acute evaluation of conversational discourse skills in traumatic brain injury

Abstract This study looked at performance on the conversational discourse checklist of the Protocole Montréal d’évaluation de la communication (D-MEC) in 195 adults with TBI of all severity hospitalized in a Level 1 Trauma Centre. To explore validity, results were compared to findings on tests of memory, mental flexibility, confrontation naming, semantic and letter category naming, verbal reasoning, and to scores on the Montreal Cognitive Assessment. The relationship to outcome as measured with the Disability Rating Scale (DRS), the Extended Glasgow Outcome Scale (GOS-E), length of stay, and discharge destinations was also determined. Patients with severe TBI performed significantly worse than mild and moderate groups (χ2KW2df = 24.435, p = .0001). The total D-MEC score correlated significantly with all cognitive and language measures (p < .05). It also had a significant moderate correlation with the DRS total score (r = −.6090, p < .0001) and the GOS-E score (r = .539, p < .0001), indicating that better performance on conversational discourse was associated with a lower disability rating and better global outcome. Finally, the total D-MEC score was significantly different between the discharge destination groups (F(3,90) = 20.19, p < . 0001). Thus, early identification of conversational discourse impairment in acute care post-TBI was possible with the D-MEC and could allow for early intervention in speech-language pathology.
Toward Increased Use of Data Worth Analyses in Groundwater Studies

Introduction Our ability to conceptually understand—and perhaps more importantly, to reliably manage—groundwater systems depends fundamentally on data. Such data include, for example, core samples from boreholes, hydraulic testing, point, transect, and aerial geophysical surveys, time series and synoptic groundwater and surface water level data, time series water quality data, spring discharge measurements, and estimates of base flow. Data available for groundwater investigations are always incomplete, so the timing, spatial distribution, and types of data at our disposal constrain our conceptual understanding and ability to manage groundwater systems. At the same time, data collection is typically is the most expensive part of an investigation. From this fundamental constraint on our science emerges a natural question: how can we identify the most informative data to collect in future investigations? Strategies toward answering these questions are referred to in various contexts, and by various researchers, as experimental design, monitoring network design, valueof-information, and data worth analyses. Here, I use the term “data worth analysis” to denote any kind of investigation that seeks to identify the most important data to collect with respect to addressing a particular question or prediction of interest, given our current state of knowledge. This essay aims to provide a mile-high view of data worth analyses in groundwater hydrology, emphasizing the main factors determining how such analyses are implemented. These main factors, in turn, are the drivers for what are in my view the promising research questions that will drive forward the state of the science in data worth analyses for groundwater applications.
ProLIF: a quantitative assay for investigating integrin cytoplasmic protein interactions and synergistic membrane effects on proteoliposomes

Integrin transmembrane heterodimeric receptors control a wide range of biological interactions by triggering the assembly of large multiprotein complexes at their cytoplasmic interface. A diverse set of methods have been used to investigate cytoplasmic interactions between integrins and intracellular proteins. These predominantly consist of peptide-based pull-downs and biochemical immuno-isolations from detergent-solubilized cell lysates. However, quantitative methods to probe integrin-protein interactions in a more biologically relevant context where the integrin is embedded within a lipid bilayer have been lacking. Here we describe a technique called ProLIF (Protein-Liposome Iinenteractions by Flow cytometry) to reconstitute recombinant integrin transmembrane domain (TMD) and cytoplasmic tail (CT) fragments on liposomes as individual α or β subunits or as αβ heterodimers and, using flow cytometry, to rapidly and quantitatively measure protein interactions with these membrane-embedded integrins. Importantly, the assay can analyse binding of fluorescent proteins directly from cell lysates without further purification steps. By combining integrins with membrane lipids to generate proteoliposomes, the effects of membrane composition such as PI(4,5)P2 presence on protein recruitment to the integrin CTs can be analyzed. ProLIF requires no specific instrumentation, apart from a standard flow cytometer and can be applied to measure a broad range of membrane-dependent protein-protein interactions with the potential for high-throughput/multiplex analyses.
The role of PET and PET-CT scanning in assessing response to neoadjuvant therapy in esophageal carcinoma.

BACKGROUND The response to neoadjuvant (radio-)chemotherapy for esophageal carcinoma is often assessed with the aid of positron-emission tomography (PET), either alone or in combination with computed tomography (PET-CT). In this review, we discuss the diagnostic validity and clinical benefit of these imaging techniques. METHODS We systematically searched the Medline, Embase, and Cochrane Library databases for randomized controlled trials (RCTs) and controlled clinical trials (CCTs) comparing PET-CT with conventional techniques such as endosonography and CT. We then determined the diagnostic validity of these methods on the basis of information from published systematic reviews, updated with further information from more recent primary studies. RESULTS We did not find any RCTs that addressed the question of the patient-relevant benefit of PET-CT. We found 20 studies of diagnostic methods, carried out on a total of 854 patients, of whom 82.2% were male. These studies had a high potential for bias. In two of them, PET-CT was directly compared with endosonography or CT. Estimates of sensitivity and specificity varied widely across studies. 54% of all patients (median value across studies) had no histopathological response to therapy at the end of treatment. Taking a reduction of the standard uptake value (SUV) by at least 35% as a threshold criterion, we found that the median negative predictive value of PET across all studies was 86.5. CONCLUSION There is no robust evidence for a patient-relevant benefit of PET and PET-CT in patients with esophageal carcinoma. PET could potentially be used to distinguish treatment responders from non-responders after the first cycle of treatment. RCTs with patient-relevant endpoints will be needed in order to determine whether this is useful.
Correlates and retrospectively reported antecedents of alexithymia.

&NA; Two experiments were conducted in order to examine the relationship between alexithymia and: 1) family environment; 2) discomfort and ambivalence experiencing and expressing emotion; and 3) dissociation. Research participants in both experiments were college students. We examined the ability to identify and communicate emotion using the Toronto Alexithymia Scale. In Experiment 1, we found that alexithymia was significantly correlated with ambivalence concerning expression of emotion (measured using the Ambivalence over Emotional Expressiveness Questionnaire) and with discomfort concerning negative emotional states (measured using a new instrument called the Emotional Experience Discomfort Scale). Higher levels of alexithymia were associated with retrospective reports of diminished family expressiveness (measured using the Expressiveness subscale of the Family Environment Scale) and with feeling less emotionally safe during childhood (measured using a new instrument called the Childhood Experiences Questionnaire). In Experiment 2, we found that alexithymia was significantly correlated with dissociative experiences (measured using the Dissociative Experiences Scale). However, alexithymia and dissociation differed in the way they were associated with retrospective reports of different aspects of family expressiveness (measured using the Family Expressiveness Questionnaire). High levels of dissociation were associated with increased negative dominant family communication. In contrast, high levels of alexithymia were associated with low levels of positive family communication.
Neurofilament heavy chain in CSF correlates with relapses and disability in multiple sclerosis

Objective: Neurodegeneration is now accepted as a pathologic hallmark of multiple sclerosis (MS). We sought to discover whether CSF levels of neurofilament heavy chain protein (NfHSMI35) correlate with disability, disease activity, or specific stages of MS. Methods: An electrochemiluminescence immunoassay was used to retrospectively measure NfHSMI35 in CSF of patients with clinically isolated syndrome (CIS) (n = 63), relapsing-remitting multiple sclerosis (RRMS) (n = 39), secondary progressive multiple sclerosis (SPMS) (n = 25), primary progressive multiple sclerosis (PPMS) (n = 23), or controls (n = 73). Cell count and CSF levels of immunoglobulin and albumin were also measured. Results: CSF levels of NfHSMI35 increased with age in controls (rs = 0.50, p < 0.0001) and CIS (rs = 0.50, p < 0.0001); this effect was less pronounced in RRMS (rs = 0.35, p = 0.027) and absent in SPMS/PPMS. After age correction, NfHSMI35 levels were found to be higher in all disease stages compared to control. Relapses were associated with higher CSF NfHSMI35 values compared with stable disease. NfHSMI35 levels correlated with EDSS scores in patients with CIS and RRMS (rs = 0.33, p = 0.001), and during relapse (rs = 0.35, p = 0.01); the correlation was most prominent in RRMS during relapse (rs = 0.54, p = 0.01). This was not the case for any of the other CSF markers examined. Conclusions: Neuronal loss is a feature of aging, and the age-dependent increase of CSF NfHSMI35 suggests that this loss accelerates over time. For MS, increased NfHSMI35 levels reflect the superimposed presence of further neurodegenerative processes. Evaluation of NfHSMI35 levels is likely to provide a useful surrogate for measuring the rate of neurodegeneration in MS. Furthermore, the dissociation of NfHSMI35 levels with biomarkers of inflammation suggests that the mechanisms responsible for their production are at least partly independent.
Cutting Construction Wastes by Prefabrication

Abstract Construction wastes have become the major source of solid wastes in Hong Kong. Thousands of tonnes of solid wastes are produced every year from construction and demolition activities. Increasing generation of these wastes has caused significant impacts on the environment and aroused growing public concerns. Therefore, the minimisation of construction wastes has become a pressing issue. This paper aims to: 1) reveal the status of construction wastes; 2) investigate the effectiveness of prefabrication in terms of waste reduction in replacing traditional wet-trade practices; 3) examine the factors that help minimize construction wastes by the adoption of prefabrication; and 4) explore the current waste reduction situations after adoption of prefabrication by comparing with in-situ construction. It investigates wastes generated from various wet-trade construction activities such as in-situ concreting, timber formwork, bricklaying, plastering, screeding, tiling, rebar fixing and bamboo scaffolding. Six major reasons for the excessive construction wastage are known to be: 1) cutting; 2) over ordering; 3) damaging during transportation; 4) losing during installation; 5) poor workmanship; and 6) change of design. From the findings of a structured interview survey of thirty-one construction practitioners, “timber formwork” is found to be having the greatest potential for cutting scrap, and wastes from “poor workmanship” can be greatly reduced by adopting prefabrication in construction. Furthermore, after the adoption of prefabrication, wastage generation can be greatly reduced in various wet-trade activities including concreting, rebar fixing, bricklaying, drywall, plastering, screeding and tiling. Especially in plastering, the waste reduction can be reduced by 100%. It is concluded that prefabrication of building components is one of the effective technologies of waste minimisation.
The role of prophylactic bilateral oophorectomy at the time of initial diagnosis of a unilateral ovarian metastasis in cases with colorectal adenocarcinoma.

BACKGROUND/AIMS In cases with a macroscopic unilateral ovarian metastasis of colorectal adenocarcinoma, a clear therapeutic policy regarding a prophylactic bilateral oophorectomy is lacking. METHODOLOGY Four cases of ovarian metastases of colorectal adenocarcinoma are presented. RESULTS Case 1 is a 63-year-old with ascending colon carcinoma, Dukes' C, and right oophorectomy due to metachronous ovarian metastasis. Case 2 is a 28-year-old with transverse colon carcinoma, Dukes' D, and right oophorectomy due to synchronous ovarian metastasis. Case 3 is a 40-year-old with rectal carcinoma, Dukes' B, and right oophorectomy due to metachronous ovarian metastasis. Case 4 is a 32-year-old with rectal carcinoma, Dukes' D, and bilateral oophorectomy due to synchronous and metachronous ovarian metastases. Later, in cases 1 and 3, in which a unilateral ovary was preserved, ovarian metastases to the preserved ovary were found and caused severe clinical symptoms. However, by that time their general condition did not permit any additional laparotomy. CONCLUSIONS Without other extensive metastases, if demonstrable diseases are found in a unilateral ovary, a prophylactic bilateral oophorectomy is recommended.
Maximizing Sparse Matrix--Vector Product Performance on RISC Based MIMD Computers

The matrix? vector product kernel can represent most of the computation in a gradient iterative solver. Thus, an efficient solver requires that the matrix? vector product kernel be fast. We show that standard approaches with Fortran or C may not deliver good performance and present a strategy involving managing the cache to improve the performance. As an example, using this approach we demonstrate that it is possible to achieve 2.5 times better performance over a Fortran implementation with an assembly coded kernel on an Intel i860. These issues are of general interest for all computer architectures but are particularly important for users of MIMD computers to achieve a useful fraction of the advertised peak performance of these machines.
Weather, Fertilizer, Previous Year Yield, and Fertilizer Levels Affect Ensuing Year Fertilizer Response of Wheat

Response to fertilizer is a function of several factors including weather, soil condition, previous year yield level, and the actual amount of fertilizer applied. The main objectives of this paper were to evaluate if cumulative precipitation (PPT), growing degree days (GDD), soil moisture (SM) and fertilizer can explain variability in long-term grain yield and fertilizer response index (RI); to assess if demand for N fertilizer is greater the ensuing year given low or high yield levels in the previous year; and to evaluate if rainfall distribution coupled with the previous year grain yield level and RI of winter wheat (Triticum aestivum L.) improves the predictability of ensuing year RI. Data from two long-term experiments located at Stillwater and Lahoma, OK were used in this report. The experimental design was a randomized complete block with four replications. Twelve (Stillwater) and thirteen (Lahoma) treatments that consisted of annual application of N, P and K inorganic fertilizers were included although selected treatments were used to address the objectives. Soil moisture at 75 cm depth was a better predictor of both grain yield (R 2 = 0.35) and RI (R 2 = 0.66) at Stillwater while SM at the 60 cm depth was significantly correlated to grain yield (R 2 = 0.39) at Lahoma. For years where the previous year yield was low, the ensuing year had a low RI while in many years where the previous yield was high; the ensuing year had a high RI in both experiments. The practical significance of these findings is that producers could theoretically adjust preplant or in-season topdress N fertilizer rates by considering the previous year yield level and the degree of response to N.
Bound Nucleotide Controls the Endonuclease Activity of Mismatch Repair Enzyme MutL*

DNA mismatch repair corrects mismatched base pairs mainly caused by replication error. Recent studies revealed that human MutL endonuclease, hPMS2, plays an essential role in the repair. However, there has been little biochemical analysis of the MutL endonuclease. In particular, it is unknown for what the MutL utilizes ATP binding and hydrolyzing activity. Here we report the detailed functional analysis of Thermus thermophilus MutL (ttMutL). ttMutL exhibited an endonuclease activity that decreased on alteration of Asp-364 in ttMutL to Asn. The biochemical characteristics of ttMutL were significantly affected on ATP binding, which suppressed nonspecific DNA digestion and promoted the mismatch- and MutS-dependent DNA binding. The inactivation of the cysteinyl residues in the C-terminal domain resulted in the perturbation in ATP-dependent regulation of the endonuclease activity, although the ATP-binding motif is located in the N-terminal domain. Complementation experiments revealed that the endonuclease activity of ttMutL and its regulation by ATP binding are necessary for DNA repair in vivo.
The Comparative Sensitivity of Intra-oral, in vitro, and Animal Models in the ‘Profile’ Evaluation of Topical Fluorides

The development of predictive and rapid methods for the assessment of the anticaries activity of topical fluorides has been a longstanding objective of caries researchers. These methods can provide useful benefits in a number of applications, ranging from the identification of novel agents to progress into clinical testing to the regulatory screening of commercial product variations. In the latter applications, combinations of test methods (so-called profiles) are used by manufacturers to prove that changes in formulations do not alter the efficacy of the products. Historically, combinations of in vitro and animal models have been used for basic research as well as for profile testing purposes; however, in recent years, the use of intra-oral or in situ models has increased. In this paper, in vitro, animal, and in situ methods are reviewed in terms of the historical basis for their development, protocols currently used in testing, and the primary advantages and limitations of each as applied to ‘profile’ applications. Recommendations are provided concerning circumstances for the appropriate use of modern test methods in formulation screening.
The Rhesus Rhadinovirus CD200 Homologue Affects Immune Responses and Viral Loads during In Vivo Infection

ABSTRACT Rhesus macaque rhadinovirus (RRV) is a gammaherpesvirus of rhesus macaque (RM) monkeys that is closely related to human herpesvirus 8 (HHV-8)/Kaposi's Sarcoma-associated herpesvirus (KSHV), and it is capable of inducing diseases in simian immunodeficiency virus (SIV)-infected RM that are similar to those seen in humans coinfected with HIV and HHV-8. Both HHV-8 and RRV encode viral CD200 (vCD200) molecules that are homologues of cellular CD200, a membrane glycoprotein that regulates immune responses and helps maintain immune homeostasis via interactions with the CD200 receptor (CD200R). Though the functions of RRV and HHV-8 vCD200 molecules have been examined in vitro, the precise roles that these viral proteins play during in vivo infection remain unknown. Thus, to address the contributions of RRV vCD200 to immune regulation and disease in vivo, we generated a form of RRV that lacked expression of vCD200 for use in infection studies in RM. Our data indicated that RRV vCD200 expression limits immune responses against RRV at early times postinfection and also impacts viral loads, but it does not appear to have significant effects on disease development. Further, examination of the distribution pattern of CD200R in RM indicated that this receptor is expressed on a majority of cells in peripheral blood mononuclear cells, including B and T cells, suggesting potentially wider regulatory capabilities for both vCD200 and CD200 that are not strictly limited to myeloid lineage cells. In addition, we also demonstrate that RRV infection affects CD200R expression levels in vivo, although vCD200 expression does not play a role in this phenomenon. IMPORTANCE Cellular CD200 and its receptor, CD200R, compose a pathway that is important in regulating immune responses and is known to play a role in a variety of human diseases. A number of pathogens have been found to modulate the CD200-CD200R pathway during infection, including human herpesvirus 8 (HHV-8), the causative agent of Kaposi's sarcoma and B cell neoplasms in AIDS patients, and a closely related primate virus, rhesus macaque rhadinovirus (RRV), which infects and induces disease in rhesus macaque monkeys. HHV-8 and RRV encode homologues of CD200, termed vCD200, which are thought to play a role in preventing immune responses against these viruses. However, neither molecule has been studied in an in vivo model of infection to address their actual contributions to immunoregulation and disease. Here we report findings from our studies in which we analyzed the properties of a mutant form of RRV that lacks vCD200 expression in infected rhesus macaques.
Prognostic Value of Computed Tomography Texture Features in Non–Small Cell Lung Cancers Treated With Definitive Concomitant Chemoradiotherapy

ObjectivesThe aim of this study was to investigate whether the computed tomography (CT) texture features of primary tumors are associated with the overall survival (OS) of non–small cell lung cancer (NSCLC) patients undergoing definitive concomitant chemoradiotherapy (CCRT). Materials and MethodsIn this retrospective study, 98 patients (83 men and 15 women; mean age, 61.9 ± 8.0 years) with unresectable NSCLCs (stage IIIA, 45; stage IIIB, 53) underwent definitive CCRT at our institution from January 2006 to December 2011. Patients were followed up for 3 years or until death. The CT texture parameters of primary tumors were extracted from contrast-enhanced CT images taken before CCRT using an in-house software program. Each texture parameter was dichotomized based on their optimal cutoff values obtained from receiver operating characteristics curve analysis. Three-year OS was compared between the dichotomized subgroups using Kaplan-Meier analysis and the log-rank test. Multivariate Cox regression analysis was performed to determine significant prognostic factors. ResultsThe 3-year cumulative survival rate was 0.51. The mean 3-year OS was 24.0 months (95% confidence interval, 21.5–26.6 months). There were no significant differences in 3-year OS according to tumor stage or histologic subtypes. However, entropy (P = 0.030), skewness (P = 0.021), and mean attenuation (P = 0.030) were shown to be significantly associated with 3-year OS. Multivariate Cox regression analysis revealed that higher entropy (adjusted hazard ratio [HR],2.31; P = 0.040), higher skewness (adjusted HR,1.92; P = 0.046), and higher mean attenuation (adjusted HR,1.93; P = 0.028) were independent predictors of decreased 3-year OS. ConclusionsComputed tomography texture features have the potential to be used as prognostic biomarkers in unresectable NSCLC patients undergoing definitive CCRT.
Chronic hepatitis C infection: a review and update on treatment strategies

HEPATITIS C VIRUS (HCV) is one of the leading causes of liver disease in Australia. It is a common cause of cirrhosis and hepatocellular carcinoma (HCC), as well as the leading reason for liver transplantation. At least 200 000 people in Australia are believed to have been infected with HCV. 1 Before the identification of this virus in 1989, this disorder was categorised as non-A, non-B hepatitis.