A v-transformed copula-based simulation model for lithological classification in an Indian copper deposit.

Copula functions are widely used for modeling multivariate dependence. Since the multivariate data may not necessarily be linear and Gaussian, the copula model is very often brought into the picture for modeling such multivariate phenomena. The lithological classification in spatial domain is a class of problems dealing with categorical variables. A generalized class of copula model is effective for such classification tasks. In this paper, a non-Gaussian copula (v-transformed copula) model has been used for lithotype classification of an Indian copper deposit. Coupling of Markov chain Monte Carlo (MCMC) simulation and copula discriminant function is performed for this purpose. Specifically, four lithotypes, e.g., granite, quartz, basic, and aplite are simulated in the case study deposit. The efficacy of v-transformed copula discriminant function-based simulation is compared with those of Gaussian copula, t copula, and sequential indicator simulations. Finally, the classification accuracy of all the approaches is examined with ground-truth lithological classes obtained from blast hole information. The results show that the v-transformed copula simulation has a relatively higher classification accuracy (76%) than those of Gaussian copula (70%), t copula (69%), and sequential indicator (70%) simulations.

The efficacy of intravenous tranexamic acid administration at induction in definitive hip fracture surgery: Is there a role?

Tranexamic acid (TXA) is a cheap and powerful drug that has several uses in surgery and is well established in elective orthopaedic surgery. At present, limited small studies have looked into its role in the acute hip fracture. Transfusion in the geriatric population presents risks and increased costs to healthcare systems around the world. Our retrospective study looks at the role of TXA administration at induction for both intracapsular fracture requiring hemiarthroplasty and our preferred method of fixation of extracapsular fracture by intramedullary nail (IM nail). We show a statistically significant reduction in the number of patients requiring transfusion as well as mean haemoglobin (Hb) drop in those undergoing hemiarthroplasty. This was not replicated in those undergoing IM nail fixation. Both groups showed no increase in 1-year mortality or thromboembolic events following TXA administration. These results support the use of TXA for hemiarthroplasty for intracapsular hip fractures over the age of 60. OBJECTIVES: The aim of this pre and post interventional study looks at the effects of intravenous administration of tranexamic acid on induction for elderly patients undergoing hemiarthroplasty or intramedullary nail fixation for hip fractures. DESIGN: Pre and post interventional, randomised observational study SETTING: Large hip fracture unit, Level 2 Trauma Centre, single centre PATIENTS: Two arms of the study looking at those aged above the age of 60 undergoing hemiarthroplasty and intramedullary nail fixation without and with tranexamic acid on induction. RESULTS: 12.1% of hemiarthroplasties required post-operative transfusion without tranexamic acid compared to 2.6% of those with tranexamic acid (n=15 vs n=3 respectively, p=0.006). Equally, the mean Hb drop in g/L is reduced in those with tranexamic acid compared to those without (mean Hb = 14.6 vs 17.7 respectively, p=0.034). This was not replicated in the IM nail group between those without and those with tranexamic acid (n=31 vs n=20 respectively, p= 0.16). The mean Hb drop in g/L was not statistically significant in the tranexamic acid arm compared to without (mean Hb = 19.2 vs mean Hb = 21.9, p=0.11). Gross reporting of thromboembolic events did not demonstrate an increase in the number of those with DVT, PE, MI or stroke. 1-year mortality was not statistically significant in either hemiarthroplasty or IM nail fixation following tranexamic acid administration. CONCLUSIONS: Tranexamic acid both statistically significantly reduces the number of patients requiring transfusion post hemiarthroplasty and also the value of mean Hb drop without appearing to increase in thromboembolic events or 1 year mortality rates. This does not appear to be emulated in the IM nail fixation although both thrombotic events and 1-year mortality rates are also not affected by administration of TXA. We propose that TXA has a role in hemiarthroplasty surgery in reducing post-operative transfusions. LEVEL OF EVIDENCE: Level 3 - retrospective cohort study.

A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT).

Background: In order to facilitate implementation of precision medicine in clinical management of cancer, there is a need to harmonise and standardise the reporting and interpretation of clinically relevant genomics data. Methods: The European Society for Medical Oncology (ESMO) Translational Research and Precision Medicine Working Group (TR and PM WG) launched a collaborative project to propose a classification system for molecular aberrations based on the evidence available supporting their value as clinical targets. A group of experts from several institutions was assembled to review available evidence, reach a consensus on grading criteria and present a classification system. This was then reviewed, amended and finally approved by the ESMO TR and PM WG and the ESMO leadership. Results: This first version of the ESMO Scale of Clinical Actionability for molecular Targets (ESCAT) defines six levels of clinical evidence for molecular targets according to the implications for patient management: tier I, targets ready for implementation in routine clinical decisions; tier II, investigational targets that likely define a patient population that benefits from a targeted drug but additional data are needed; tier III, clinical benefit previously demonstrated in other tumour types or for similar molecular targets; tier IV, preclinical evidence of actionability; tier V, evidence supporting co-targeting approaches; and tier X, lack of evidence for actionability. Conclusions: The ESCAT defines clinical evidence-based criteria to prioritise genomic alterations as markers to select patients for targeted therapies. This classification system aims to offer a common language for all the relevant stakeholders in cancer medicine and drug development.

Clinical and molecular characterization of patients with cancer of unknown primary in the modern era.

BACKGROUND: On the basis of historical data, patients with cancer of unknown primary (CUP) are generally assumed to have a dismal prognosis with overall survival of less than 1 year. Treatment is typically cytotoxic chemotherapy guided by histologic features and the pattern of metastatic spread. The purpose of this study was to provide a clinical and pathologic description of patients with CUP in the modern era, to define the frequency of clinically actionable molecular alterations in this population, to determine how molecular testing can alter therapeutic decisions, and to investigate novel uses of next-generation sequencing in the evaluation and treatment of patients with CUP. PATIENTS AND METHODS: Under Institutional Review Board approval, we identified all CUP patients evaluated at our institution over a recent 2-year period. We documented demographic information, clinical outcomes, pathologic evaluations, next-generation sequencing of available tumor tissue, use of targeted therapies, and clinical trial enrollment. RESULTS: We identified 333 patients with a diagnosis of CUP evaluated at our institution from 1 January 2014 through 30 June 2016. Of these patients, 150 had targeted next-generation sequencing carried out on available tissue. Median overall survival in this cohort was 13 months. Forty-five of 150 (30%) patients had potentially targetable genomic alterations identified by tumor molecular profiling, and 15 of 150 (10%) received targeted therapies. Dominant mutation signatures were identified in 21 of 150 (14%), largely implicating exogenous mutagen exposures such as ultraviolet radiation and tobacco. CONCLUSIONS: Patients with CUP represent a heterogeneous population, harboring a variety of potentially targetable alterations. Next-generation sequencing may provide an opportunity for CUP patients to benefit from novel personalized therapies.

Oncologist use and perception of large panel next-generation tumor sequencing.

BACKGROUND: Genomic profiling is increasingly incorporated into oncology research and the clinical care of cancer patients. We sought to determine physician perception and use of enterprise-scale clinical sequencing at our center, including whether testing changed management and the reasoning behind this decision-making. PATIENTS AND METHODS: All physicians who consented patients to MSK-IMPACT, a next-generation hybridization capture assay, in tumor types where molecular profiling is not routinely performed were asked to complete a questionnaire for each patient. Physician determination of genomic 'actionability' was compared to an expertly curated knowledgebase of somatic variants. Reported management decisions were compared to chart review. RESULTS: Responses were received from 146 physicians pertaining to 1932 patients diagnosed with 1 of 49 cancer types. Physicians indicated that sequencing altered management in 21% (331/1593) of patients in need of a treatment change. Among those in whom treatment was not altered, physicians indicated the presence of an actionable alteration in 55% (805/1474), however, only 45% (362/805) of these cases had a genomic variant annotated as actionable by expert curators. Further evaluation of these patients revealed that 66% (291/443) had a variant in a gene associated with biologic but not clinical evidence of actionability or a variant of unknown significance in a gene with at least one known actionable alteration. Of the cases annotated as actionable by experts, physicians identified an actionable alteration in 81% (362/445). In total, 13% (245/1932) of patients were enrolled to a genomically matched trial. CONCLUSION: Although physician and expert assessment differed, clinicians demonstrate substantial awareness of the genes associated with potential actionability and report using this knowledge to inform management in one in five patients. CLINICAL TRIAL NUMBER: NCT01775072.

Estrogen receptor beta1 and the beta2/betacx isoforms in nonneoplastic endometrium and in endometrioid carcinoma.

Estrogen receptor beta (ERbeta) has five carboxyl-terminal (C-terminal) isoforms derived from alternative splicing. ERbeta1 is the wild-type receptor whereas ERbeta2/betacx lacks the activation function (AF)-2 core essential for ligand-dependent transcriptional activation and so behaves as a dominant-negative receptor affecting the function of ERalpha. The objective of this study was to analyze the expression of ERbeta1 and ERbeta2/betacx isoforms in nonneoplastic endometrium and endometrioid carcinoma. The study was conducted on samples of 22 proliferative endometrium, 15 secretory endometrium, 20 simple hyperplasia (without atypia), and 26 endometrioid carcinomas. The transcript and protein levels were determined by semiquantitative reverse transcriptase-polymerase chain reaction and immunohistochemistry, respectively. For the detection of ERbeta2/betacx protein, a polyclonal antibody was raised to its unique C-terminus, characterized, and used in immunohistochemistry. The two ERbeta isoforms are expressed in the proliferative and secretory phase endometrium with no significant change in their relative levels. The levels of the ERbeta1 isoform were lower as compared to the levels of ERbeta2 in all the groups studied. Expression of ERbeta2/betacx was decreased in endometrioid carcinoma as compared to proliferative endometrium (P < 0.01). A significant decrease of the ERbeta2/ERbetacx transcript was observed with higher grade tumors (P = 0.041). Progesterone receptor (PR) expression was not influenced by either of the ERbeta isoforms which was observed by logistic regression analysis in all the groups. The coexpression of ERbeta2/betacx with ERalpha did not affect PR levels (logistic regression analysis). Thus, we conclude in the human endometrium, there is significant ERbeta2/betacx isoform expression and alterations in its levels could be involved in endometrial cancer progression.

Is perioperative blood transfusion a risk factor for mortality or infection after hip fracture?

OBJECTIVES: To assess whether allogeneic blood transfusion in the perioperative period is associated with changes in mortality or complication rates in patients undergoing surgical treatment for hip fracture (proximal femoral fracture). DESIGN: Retrospective case-control series, all patients followed up for 1 year or until death. SETTING: District General Hospital in Peterborough, UK. PATIENTS PARTICIPANTS: Three thousand six hundred twenty-five consecutive patients admitted and operated for hip fracture (proximal femoral fracture) during July 1989 to January 2002 (151 months); 1068 (29.9%) received a perioperative allogeneic blood transfusion. MAIN OUTCOME MEASURES: Thirty- 120-, and 365-day mortality, deep and superficial wound infection rates. RESULTS: Overall mortality for all patients at 1 year post fracture was 28.2% (1007 patients). Transfusion was associated with a statistically significant increase in mortality from 120 days onward after hip fracture. However, when this was adjusted with a statistical regression model for baseline characteristics and confounding variables, this difference became statistically insignificant (P = 0.17). Infection rates in the transfusion group were 2.0% for superficial infection and 0.9% for deep infection compared with 1.9% and 0.6%, respectively, in the nontransfusion group. These figures were not statistically significantly different. Other complications of deep venous thrombosis, chest infection, and congestive cardiac failure showed no statistically significant increase in those patients who received transfusion. CONCLUSIONS: Our data suggest that transfusion is not associated with a change in mortality or infection rates in the hip-fracture patient.

A novel 14-3-3 gene is osmoregulated in gill epithelium of the euryhaline teleost Fundulus heteroclitus.

We have cloned and analyzed the full-length coding sequence and 3' untranslated region (UTR) of a unique 14-3-3 gene of the euryhaline teleost Fundulus heteroclitus, which we named 14-3-3.a. Phylogenetic analysis of the deduced amino acid sequence revealed that the 14-3-3.a gene product is most similar to vertebrate 14-3-3 zeta and beta, yet it displays considerable divergence to known classes of vertebrate 14-3-3 isoforms. The N and C termini of 14-3-3.a are the most unique regions, whereas the amino acid residues forming the amphipathic ligand-binding groove are highly conserved. F. heteroclitus 14-3-3.a mRNA expression is high in gill epithelium, moderate in intestine and brain, and low in gonads, white muscle and heart. Because 14-3-3 proteins are important molecular scaffolds and cofactors for phosphoproteins and signaling complexes, the high level of 14-3-3.a expression in gill epithelium of the euryhaline teleost F. heteroclitus suggests that it is crucial for signal transduction in gill epithelial cells. We provide evidence that 14-3-3.a is involved in osmosensory signal transduction by showing that its mRNA and protein levels in gill epithelium, but not in any other tissue analyzed, increase two- to fourfold within 24h of salinity transfer of fish from sea water to fresh water. These data are clear evidence for an important role of 14-3-3.a in the remodeling of gill epithelium during transition of euryhaline fish between plasma-hyperosmotic and plasma-hypoosmotic environments.

Hyperosmolality in the form of elevated NaCl but not urea causes DNA damage in murine kidney cells.

This study demonstrates, by using neutral comet assay and pulsed field gel electrophoresis, that hyperosmotic stress causes DNA damage in the form of double strand breaks (dsb). Different solutes increase the rate of DNA dsb to different degrees at identical strengths of hyperosmolality. Hyperosmolality in the form of elevated NaCl (HNa) is most potent in this regard, whereas hyperosmolality in the form of elevated urea (HU) does not cause DNA dsb. The amount of DNA dsb increases significantly as early as 15 min after the onset of HNa. By using neutral comet and DNA ladder assays, we show that this rapid induction of DNA damage is not attributable to apoptosis. We demonstrate that renal inner medullary cells are able to efficiently repair hyperosmotic DNA damage within 48 h after exposure to hyperosmolality. DNA repair correlates with cell survival and is repressed by 25 microM LY294002, an inhibitor of DNA-activated protein kinases. These results strongly suggest that the hyperosmotic stress resistance of renal inner medullary cells is based not only on adaptations that protect cellular proteins from osmotic damage but, in addition, on adaptations that compensate DNA damage and maintain genomic integrity.

Maintenance of genomic integrity in mammalian kidney cells exposed to hyperosmotic stress.

Changes in environmental salinity/osmolality impose an osmotic stress upon cells because, if left uncompensated, such changes will alter the conserved intracellular ionic milieu and macromolecular density, for which cell metabolism in most extant cells has been optimized. Cell responses to osmotic stress include rapid posttranslational and slower transcriptional events for the compensatory regulation of cell volume, intracellular electrolyte concentrations, and protein stability/activity. Changes in external osmolality are perceived by osmosensors that control the activation of signal transduction pathways giving rise to the above responses. We have recently shown that the targets of such pathways include cell cycle-regulatory and DNA damage-inducible genes (reviewed in Kültz, D., 2000. Environmental stressors and gene responses, Elsevier, Amsterdam. pp 157-179). Moreover, recent evidence suggests that hyperosmotic stress causes chromosomal aberrations and DNA double-strand breaks in mammalian cells. We propose that the modulation of cell cycle checkpoints and the preservation of genomic integrity are important aspects of cellular osmoprotection and as essential for cellular osmotic stress resistance as the capacity for cell volume regulation and maintaining inorganic ion homeostasis and protein stability/activity.

Differential roles in the neuronal network for audiogenic seizures are observed among the inferior colliculus subnuclei and the amygdala.

The inferior colliculus (IC) is established as the initiation site within the neuronal network for audiogenic seizures (AGS), but the relative importance of the IC subnuclei in AGS is controversial. The lateral and basolateral subdivisions of the amygdala are implicated in the expansion of the AGS network that occurs during AGS kindling. However, the role of the amygdala in the AGS network in nonkindled AGS is unknown. NMDA receptors are implicated in modulation of AGS and in neurotransmission in both the IC and amygdala. Therefore, changes in AGS severity in genetically epilepsy-prone rats (GEPR-9s) were examined after bilateral focal microinjection into IC subnuclei or lateral/basolateral subdivisions of the amygdala of a competitive NMDA receptor antagonist, 3-((+)-2-carboxypiperazine-4-yl)propyl-1-phosphonic acid (CPP). Blockade of AGS in IC central nucleus (ICc) and external cortex (ICx) was observed at identical doses of CPP, but these doses were ineffective in IC dorsal cortex (ICd). Microinjection of CPP into the amygdala did not produce significant changes in AGS severity except at doses 20 times those effective in IC. The latter data contrast with the anticonvulsant effects of amygdala microinjections on seizure severity in kindled AGS reported previously. The present data in concord with neuronal recording studies of these nuclei suggest that the ICc is the most critical site in AGS initiation, the ICx in propagation, and that the ICd plays a lesser role in the AGS network. The amygdala does not appear to play a requisite role in the neuronal network for AGS in animals that have not been subjected to AGS kindling.

Time course of transient expression of GDNF protein in rat granule cells of the bilateral dentate gyri after unilateral intrahippocampal kainic acid injection.

We examined the time course of expression of glial cell line-derived neurotrophic factor (GDNF) protein in the granule cells of the dentate gyrus following unilateral intrahippocampal injection of kainic acid (KA). Recurrent behavioral seizures were observed approximately 1 h after KA injection, which lasted for 4-6 h. GDNF immunoreactivity began to increase bilaterally in the granule cells within 3 h after KA injection, continued to increase until post-injection day (PID) 4, and returned to the control level by PID 7. The results suggest that the increase of GDNF protein in the granule cells may be ascribable to seizures induced by the KA injection. The increase of GDNF protein might promote survival of the granule cells after the intrahippocampal KA injection.

NMDAR2 upregulation precedes mossy fiber sprouting in kainate rat hippocampal epilepsy.

Following intrahippocampal (hilar) kainic acid (KA) lesions in rats, NMDAR2A/B receptor proteins are upregulated significantly in the inner molecular layer (IML) of the dentate gyrus by post-injection day 5. By contrast, the aberrant mossy fibers which reinnervate the IML remained in the subgranular zone before sprouting and synapsing in the IML, which occurs at approximately post-KA day 17. For 40 days thereafter, this mossy fiber ingrowth progressed, while the increased NMDAR2A/B (receptors) immunoreactivity remained at the same densities. These results suggest that new NMDAR2A/B proteins in granule cell dendrites are limited to the IML, which is the eventual site for MF hyperinnervation, neosynaptogenesis, and recurrent synaptic hyperexcitability.

Postnatal expressions of non-phosphorylated and phosphorylated neurofilament proteins in the rat hippocampus and the Timm-stained mossy fiber pathway.

Neurofilament proteins (NFPs), the cytoskeletal proteins that are essential for axogenesis and maintenance of neuron shape in the nervous system, were studied for their spatial distributions at nine postnatal days (PN 3, 5, 7, 10, 14, 17, 21, 28, and 120). Simultaneously non-phosphorylated (SMI-32; 150/200 kDa; Sternberger) and phosphorylated (SMI-31; 200 kDa) NFP immunoreactivity in the entire developing rat hippocampus was studied, quantified, and compared to that of mossy fiber (MF) axons and terminals using Neo-Timm's histochemistry, the most selective, sensitive, and reproducible technique. Differential developmental expressions were observed between the two NFP states. SMI-32 was initially expressed on PN 3 only in the perikarya of pyramidal neurons in CA3. As early as PN 5, SMI-31 appeared in the MF pathway, in parallel to the growth of MF axons. By contrast, SMI-32 did not appear at any age in the MF pathway, including the MF terminal zone of stratum lucidum. At PN 14, the distribution of both NFPs in the MF system (MFs and their target neurons, i.e., CA3/CA4 pyramidal neurons and hilar neurons) was nearly complete; however, the peak densities of SMI-32 and SMI-31 were later at PN 21 and statistically equal to the most adult level (PN 120). The temporal regulation and maximal levels of SMI-32 and SMI-31 expressions on MF target neurons (CA3: SMI-32) and in the MF terminal zone (stratum lucidum: SMI-31) were nearly parallel to the progressive and rapid PN growth of the MF axons and terminals occurring between PN 14 and PN 17, suggesting that the mechanisms for maturation of MF synaptogenesis occur after PN 17.

Comparison of neuronal response patterns in the external and central nuclei of inferior colliculus during ethanol administration and ethanol withdrawal.

Convulsive seizures during ethanol withdrawal (ETX) in rodents can be precipitated by acoustic stimulation. The inferior colliculus (IC) is strongly implicated in the neuronal network for these audiogenic seizures (AGS) in animals undergoing ETX. Previous evidence indicates that the central nucleus of IC (ICc) is important in AGS initiation in ETX, but the ICc does not project directly to motor pathways. The external nucleus of IC (ICx) receives convergent output from a broad range of ICc neurons, which is not tonotopically organized, and projects to several nuclei with major motor connections. Lesion, neuroanatomical, and stimulation experiments suggest the involvement of the ICx in the AGS network in several forms of AGS, including ETX. The present study examined ICx neuronal firing patterns in awake behaving rats during ethanol administration and during ETX to examine the role of this structure directly. ICx neuronal responses during both ethanol intoxication and ETX were significantly suppressed as compared to pre-ethanol responses. ICx neuronal responsiveness was reduced (habituated) at faster (>0.25 Hz) rates of stimulus presentation. However, immediately prior to the onset of AGS, there was an increase in ICx neuronal responses that continued into the wild running phase of AGS. This increase in neuronal responses temporally corresponded to the sustained ICc neuronal responses during ETX just prior to AGS. The enhanced ICx neuronal responsiveness may be mediated, in part, by changes in GABA and glutamate receptor regulation previously observed during ETX. The net result of these changes involves a functional reversal of response habituation normally observed in ICx neurons. These data illuminate the nature of the changes in ICx neuronal function that serves to transmit the sensory input that originates in the ICc and propagates seizure to the brainstem AGS network nuclei responsible for the convulsive motor behaviors of ETX seizures.

Aberrant neuronal responsiveness in the genetically epilepsy-prone rat: acoustic responses and influences of the central nucleus upon the external nucleus of inferior colliculus.

The inferior colliculus (IC) central nucleus (ICc), is critical for audiogenic seizure (AGS) initiation in the genetically epilepsy-prone rat (GEPR). The ICc lacks direct motor outputs but sends a major projection to the external nucleus of IC (ICx), which does project to the sensorimotor integration nuclei within the AGS neuronal network. The present study compared acoustic responses of ICx neurons in the GEPR and normal anesthetized rat and evaluated whether the GEPR exhibits functional abnormalities in the pathway from ICc to ICx. There is a significantly greater incidence of sustained repetitive response patterns to the acoustic stimulus in GEPR ICx neurons (75%) than in normal ICx neurons (24%). Following unilateral microinjection of N-methyl-D-aspartate (NMDA) into the contralateral ICc, acoustically-evoked ICx excitation and inhibition were each increased in normal animals, which is consistent with the mixed projections previously reported in this pathway and observed with electrical stimulation in the present study. The NMDA-induced ICx firing increase may be relevant to AGS, since, in previous studies, bilateral focal microinjection of NMDA into the ICc induced AGS susceptibility in normal rats [23]. However, the incidence and degree of the ICx neuronal response changes after NMDA microinjection was not abnormal in the GEPR. These data suggest that the hyperresponsiveness of ICx neurons may not involve abnormal transmission between the ICc and ICx, despite the elevated ICx neuronal responses to acoustic stimuli. However, the ICx hyperresponsivess of the GEPR, which is likely due to the known decrease in effectiveness of GABA-mediated inhibition in GEPR neurons, may be a major mechanism subserving the critical role that this structure plays in the AGS network.

Bilateral kainic acid lesions in the rat hilus induce non-linear additive mossy fiber neoinnervation.

Kainic acid (KA) lesions of the rat hilus model hippocampal sclerosis and temporal lobe epilepsy. Unilateral hilar cell loss denervates the associational afferents normally projecting to the inner molecular layer (IML) granule cell dendrites, followed by ipsilateral mossy fiber (MF) sprouting. Hilar neurons also project through the hippocampal commissure to the contralateral IML. This study compared densities of IML MF sprouting following unilateral versus bilateral low dose KA lesions, using Neo-Timm stain 30 days later. Unilateral KA (0.4 microg) caused only dense ipsilateral MF sprouting. Bilateral lesions with lower doses of KA (0.1 with 0.2 or 0.3 microg) induced dense bilateral MF sprouting. However, the same low doses of KA injected unilaterally did not induce significant sprouting ipsilaterally or contralaterally. These data show that denervations of both associational and commissural afferents to the same IML dendritic zones of granule cells induce non-linear, additive bilateral MF neoinnervations.