Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing data structures in high-level programs: new directions for extensible compilers based on staging

High level data structures are a cornerstone of modern programming and at the same time stand in the way of compiler optimizations. In order to reason about user- or library-defined data structures compilers need to be extensible. Common mechanisms to extend compilers fall into two categories. Frontend macros, staging or partial evaluation systems can be used to programmatically remove abstraction and specialize programs before they enter the compiler. Alternatively, some compilers allow extending the internal workings by adding new transformation passes at different points in the compile chain or adding new intermediate representation (IR) types. None of these mechanisms alone is sufficient to handle the challenges posed by high level data structures. This paper shows a novel way to combine them to yield benefits that are greater than the sum of the parts. Instead of using staging merely as a front end, we implement internal compiler passes using staging as well. These internal passes delegate back to program execution to construct the transformed IR. Staging is known to simplify program generation, and in the same way it can simplify program transformation. Defining a transformation as a staged IR interpreter is simpler than implementing a low-level IR to IR transformer. With custom IR nodes, many optimizations that are expressed as rewritings from IR nodes to staged program fragments can be combined into a single pass, mitigating phase ordering problems. Speculative rewriting can preserve optimistic assumptions around loops. We demonstrate several powerful program optimizations using this architecture that are particularly geared towards data structures: a novel loop fusion and deforestation algorithm, array of struct to struct of array conversion, object flattening and code generation for heterogeneous parallel devices. We validate our approach using several non trivial case studies that exhibit order of magnitude speedups in experiments.
Comparison of the feeding apparatus and diet of European sardines Sardina pilchardus of Atlantic and Mediterranean waters: ecological implications.

In this study, the feeding apparatus (gill rakers, GR) and the diet composition of European sardine Sardina pilchardus populations living in two contrasting environments were compared: the upwelling area off western Iberia and the comparatively less productive region of the north-western Mediterranean Sea. The importance of local adaptations in the trophic ecology of this species was estimated. Sardina pilchardus from the Atlantic Iberian coast and from the north-western Mediterranean Sea have clear differences in the feeding apparatus and diet compositions. Those from the Atlantic Iberian coast have significantly more GRs than S. pilchardus of the same size range in the Mediterranean Sea. While S. pilchardus from the Mediterranean Sea mostly depend on prey ranging between 750-1500 and 3000-4000 µm, corresponding mostly to cladocerans, decapods and copepods, those from the Atlantic depend on smaller prey (50-500 and 1000-1500 µm) that include phytoplankton and copepods, particularly during summer months, and S. pilchardus eggs during the winter. The marked difference between the trophic ecology of S. pilchardus in the two areas studied appears to have originated from different dietary strategies that the two populations have adopted in contrasting feeding environments. These differences are shown to profoundly affect the size and quality of prey consumed, and the effect of cannibalism on the populations.
AN ASSOCIATION BETWEEN A FLORAL TRAIT AND INBREEDING DEPRESSION

Abstract Inbreeding depression is a general phenomenon that is well documented in many plants and animals. Furthermore, it is generally considered to be the driving force behind mating-system evolution. Traditionally, the focus has been on the mean level of inbreeding depression in populations. However, more recently, the variation in inbreeding depression among individuals within populations has been shown to be influential in mating-system evolution. One set of theories predicts that genetic associations will develop between a mating-system locus and loci causing inbreeding depression, whereas another suggests either that no such association will occur or that it will be difficult to detect empirically. Here, we focus on variation in inbreeding depression among individuals and present empirical evidence of a genetic association between genes causing inbreeding depression and a floral trait influencing the mating system (i.e., selfing rate). We found a positive association between inbreeding depression and herkogamy (the degree to which the stigma and anthers are separated) in an annual plant, Gilia achilleifolia. These results are consistent with theory predicting that an individual's history of inbreeding will affect its level of inbreeding depression and highlight the potential importance of genetic associations between selfing-modifier traits and viability in mating-system evolution. Corresponding Editor: K. Holsinger
Activation of the Feeding Reflex in Hydra littoralis

A simple and accurate quantitative assay of the glutathione-activated feeding reflex in Hydra is described. The results show: (a) There are a limited number of receptor-effector systems, probably localized in the area immediately around the mouth and on the tentacles. (b) Concentrations of glutathione greater than 5 x 10-6 M activate all these systems; 10-5 M glutathione elicits a half-maximum response. (c) Glutathione must be constantly present at the receptor site in order for a response to occur. (d) The response stops in the presence of excess glutathione because of some change within the Hydra, and not as a result of any alteration to the glutathione. The present state of knowledge concerning the mechanism by which glutathione combines with and activates the glutathione receptor to elicit the feeding reflex is summarized.
Hypovitaminosis D is associated with lower urinary tract symptoms and benign prostate hyperplasia in type 2 diabetes

Lower urinary tract symptoms (LUTS) may develop more commonly in men with type 2 diabetes mellitus (T2DM). LUTS are often associated with benign prostate hyperplasia (BPH), in general population. An association between LUTS and hypovitaminosis D, and between hypovitaminosis D and type 2 diabetes (T2DM), has also been suggested. Thus, we aim to evaluate possible relationships between hypovitaminosis D, LUTS, and BPH in T2DM men. In this prospective observational study, 67 T2DM males (57.9 ± 9.28 years) underwent medical history collection, International Prostate Symptom Score (IPSS) questionnaire, that allows the identification and grading of LUTS, physical examination, biochemical/hormonal blood tests (fasting plasma glucose, glycated haemoglobin, total cholesterol, high‐density lipoprotein cholesterol, triglycerides, creatinine, LH, total testosterone, estradiol (E2), 25‐OH‐vitamin D, PTH, calcium, phosphate, and PSA) and ultrasound transrectal prostate examination. Subdividing patients into three groups, on the base of 25‐OH‐vitamin D concentration (sufficiency ≥50; insufficiency >25 < 50; and deficiency ≤25 nm), a significant progressive increase of prostate volume (p = 0.037), IPSS score (p = 0.019), diastolic blood pressure (p = 0.018), and a significant decrease in HDL cholesterol (p = 0.038) were observed. 25‐OH‐Vitamin D levels were inversely correlated with both IPSS (R = −0.333; p = 0.006) and prostate volume (R = −0.311; p = 0.011). At multivariate analysis, hypovitaminosis D remained an independent predictor of both IPSS and prostate volume. In conclusion, we showed, for the first time, an association between 25‐OH‐vitamin D deficiency, LUTS, and BPH in T2DM men.
A Comparison of Immunohistochemical Assays and FISH in Detecting the ALK Translocation in Diagnostic Histological and Cytological Lung Tumor Material

Introduction: Detection of the ALK rearrangement in a solid tumor gives these patients the option of crizotinib as an oral form of anticancer treatment. The current test of choice is fluorescence in situ hybridization (FISH), but various cheaper and more convenient immunohistochemical (IHC) assays have been proposed as alternatives. Methods: Fifteen FISH-positive cases from patients, seven with data on crizotinib therapy and clinical response, were evaluated for the presence of ALK protein using three different commercially available antibodies: D5F3, using the proprietary automated system (Ventana), ALK1 (Dako), and 5A4 (Abcam). A further 14 FISH-negative and three uncertain (<15% rearrangement detected) cases were also retrieved. Of the total 32 specimens, 17 were excisions and 15 were computed tomography-guided biopsies or cytological specimens. All three antibodies were applied to all cases. Antibodies were semiquantitatively scored on intensity, and the proportion of malignant cells stained was documented. Cutoffs were set by receiver operating curve analysis for positivity to optimize correct classification. Results: All three IHC assays were 100% specific but sensitivity did vary: D5F3 86%, ALK 79%, 5A4 71%. Intensity was the most discriminating measure overall, with a combination of proportion and intensity not improving the test. No FISH-negative IHC-positive cases were seen. Two FISH-positive cases were negative with all three IHC assays. One of these had been treated with crizotinib and had failed to show clinical response. The other harbored a second driving mutation in the EGFR gene. Conclusions: IHC with all three antibodies is especially highly specific (100%) although variably sensitive (71%-86%), specifically in cases with scanty material. D5F3 assay was most sensitive in these latter cases. Occasional cases are IHC-positive but FISH-negative, suggesting either inaccuracy of one assay or occasional tumors with ALK rearrangement that do not express high levels of ALK protein.
Association between urine osmolality and specific gravity in dogs and the effect of commonly measured urine solutes on that association.

OBJECTIVE To determine the association between urine osmolality and specific gravity (USG) in dogs and to evaluate the effect of commonly measured urine solutes on that association. ANIMALS 60 dogs evaluated by an internal medicine service. PROCEDURES From each dog, urine was obtained by cystocentesis and USG was determined with a refractometer. The sample was divided, and one aliquot was sent to a diagnostic laboratory for urinalysis and the other was frozen at -80°C until osmolality was determined. Urine samples were thawed and osmolality was measured in duplicate with a freezing-point depression osmometer. The correlation between mean urine osmolality and USG was determined; the effect of pH, proteinuria, glucosuria, ketonuria, bilirubinuria, and hemoglobinuria on this relationship was investigated with multiple regression analysis. RESULTS The Pearson correlation coefficient between urine osmolality and USG was 0.87. The final multivariable regression model for urine osmolality included USG and the presence of ketones; ketonuria had a small negative association with urine osmolality. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated a strong linear correlation between osmolality and USG in urine samples obtained from dogs with various pathological conditions, and ketonuria had a small negative effect on that correlation.
Improved human–robot team performance through cross-training, an approach inspired by human team training practices

We design and evaluate a method of human–robot cross-training, a validated and widely used strategy for the effective training of human teams. Cross-training is an interactive planning method in which team members iteratively switch roles with one another to learn a shared plan for the performance of a collaborative task. We first present a computational formulation of the robot mental model, which encodes the sequence of robot actions necessary for task completion and the expectations of the robot for preferred human actions, and show that the robot model is quantitatively comparable to the mental model that captures the inter-role knowledge held by the human. Additionally, we propose a quantitative measure of robot mental model convergence and an objective metric of model similarity. Based on this encoding, we formulate a human–robot cross-training method and evaluate its efficacy through experiments involving human subjects ( n = 60 ) . We compare human–robot cross-training to standard reinforcement learning techniques, and show that cross-training yields statistically significant improvements in quantitative team performance measures, as well as significant differences in perceived robot performance and human trust. Finally, we discuss the objective measure of robot mental model convergence as a method to dynamically assess human errors. This study supports the hypothesis that the effective and fluent teaming of a human and a robot may best be achieved by modeling known, effective human teamwork practices.
Foramen Ovale Closure Is a Process of Endothelial-to-Mesenchymal Transition Leading to Fibrosis

Patent foramen ovale (PFO) is an atrial septal deformity present in around 25% of the general population. PFO is associated with major causes of morbidity, including stroke and migraine. PFO appears to be heritable but genes involved in the closure of foramen ovale have not been identified. The aim of this study is to determine molecular pathways and genes that are responsible to the postnatal closure of the foramen ovale. Using Sprague-Dawley rat hearts as a model we analysed the dynamic histological changes and gene expressions at the foramen ovale region between embryonic day 20 and postnatal day 7. We observed a gradual loss of the endothelial marker PECAM1, an upregulation of the mesenchymal marker vimentin and α-smooth muscle actin, the elevation of the transcription factor Snail, and an increase of fibroblast activation protein (FAP) in the foramen ovale region as well as the deposition of collagen-rich connective tissues at the closed foramen ovale, suggesting endothelial-to-mesenchymal transition (EndMT) occurring during foramen ovale closure which leads to fibrosis. In addition, Notch1 and Notch3 receptors, Notch ligand Jagged1 and Notch effector HRT1 were highly expressed in the endocardium of the foramen ovale region during EndMT. Activation of Notch3 alone in an endothelial cell culture model was able to drive EndMT and transform endothelial cells to mesenchymal phenotype. Our data demonstrate for the first time that FO closure is a process of EndMT-mediated fibrosis, and Notch signalling is an important player participating in this process. Elucidation of the molecular mechanisms of the closure of foramen ovale informs the pathogenesis of PFO and may provide potential options for screening and prevention of PFO related conditions.
Airborne or Fomite Transmission for Norovirus? A Case Study Revisited

Norovirus infection, a highly prevalent condition associated with a high rate of morbidity, comprises a significant health issue. Although norovirus transmission mainly occurs via the fecal-oral and vomit-oral routes, airborne transmission has been proposed in recent decades. This paper re-examines a previously described norovirus outbreak in a hotel restaurant wherein airborne transmission was originally inferred. Specifically, the original evidence that suggested airborne transmission was re-analyzed by exploring an alternative hypothesis: could this outbreak instead have occurred via fomite transmission? This re-analysis was based on whether fomite transmission could have yielded similar attack rate distribution patterns. Seven representative serving pathways used by waiters were considered, and the infection risk distributions of the alternative fomite transmission routes were predicted using a multi-agent model. These distributions were compared to the reported attack rate distribution in the original study using a least square methods approach. The results show that with some reasonable assumptions of human behavior patterns and parameter values, the attack rate distribution corresponded well with that of the infection risk via the fomite route. This finding offers an alternative interpretation of the transmission routes that underlay this particular norovirus outbreak and an important consideration in the development of infection control guidelines and the investigation of similar norovirus outbreaks in future.
Task Behaviors During Web Search: The Difficulty of Assigning Labels

By examining searcher behavior on a large search engine, we have identified seven basic kinds of task behaviors that can be observed in web search session logs. In the studies reported, we first manually labeled 700 complete web sessions, and then subsequently had 23 searchers self-label 252 days of their own sessions to give an accurate picture of what kinds of tasks people are doing when they search. From these two studies, we have found that the most accurate labeling of search task session data is done by the searchers themselves, and that it is very difficult for an external observer or automatic classifier to infer where the task boundaries are or what the actual user task goal is.
GrpL, a Grb2-related Adaptor Protein, Interacts with SLP-76 to Regulate Nuclear Factor of Activated T Cell Activation

Propagation of signals from the T cell antigen receptor (TCR) involves a number of adaptor molecules. SH2 domain–containing protein 76 (SLP-76) interacts with the guanine nucleotide exchange factor Vav to activate the nuclear factor of activated cells (NF-AT), and its expression is required for normal T cell development. We report the cloning and characterization of a novel Grb2-like adaptor molecule designated as Grb2-related protein of the lymphoid system (GrpL). Expression of GrpL is restricted to hematopoietic tissues, and it is distinguished from Grb2 by having a proline-rich region. GrpL can be coimmunoprecipitated with SLP-76 but not with Sos1 or Sos2 from Jurkat cell lysates. In contrast, Grb2 can be coimmunoprecipitated with Sos1 and Sos2 but not with SLP-76. Moreover, tyrosine-phosphorylated LAT/pp36/38 in detergent lysates prepared from anti-CD3 stimulated T cells associated with Grb2 but not GrpL. These data reveal the presence of distinct complexes involving GrpL and Grb2 in T cells. A functional role of the GrpL–SLP-76 complex is suggested by the ability of GrpL to act alone or in concert with SLP-76 to augment NF-AT activation in Jurkat T cells.
Helicobacter pylori“Rescue” Therapy After Failure of Two Eradication Treatments

Nowadays, apart from having to know well first‐line eradication regimens, we must also be prepared to face Helicobacter pylori treatment failures. Therefore, in designing a treatment strategy we should not focus on the results of primary therapy alone, but also on the final – overall – eradication rate. After failure of a combination of proton pump inhibitor (PPI), amoxicillin, and clarithromycin, the use of empirical quadruple therapy (PPI–bismuth–tetracycline–metronidazole), has been generally used as the optimal second‐line therapy. Even after two consecutive failures, several studies have demonstrated that H. pylori eradication can finally be achieved in almost all patients if several “rescue” therapies are consecutively given. It seems that performing culture even after a second eradication failure may not be necessary, as it is possible to construct an overall strategy to maximize H. pylori eradication, based on the different possibilities of empirical treatment (when antibiotic susceptibilities are unknown). Thus, if one does not want to perform culture before the administration of the third treatment after failure of the first two, different empirical treatments exist, including regimens based on: 1, amoxicillin (amoxicillin–PPI at high doses); 2, amoxicillin plus tetracycline (PPI–bismuth–tetracycline–amoxicillin, or ranitidine–bismuth–citrate–tetracyline–amoxicillin); 3, rifabutin (rifabutin–amoxicillin–PPI); 4, levofloxacin (levofloxacin–amoxicillin–PPI); and 5, furazolidone (furazolidone–bismuth–tetracycline–PPI).
Angiogenesis in Ischemic Stroke and Angiogenic Effects of Chinese Herbal Medicine

Stroke is one of the major causes of death and adult disability worldwide. The underlying pathophysiology of stroke is highly complicated, consisting of impairments of multiple signalling pathways, and numerous pathological processes such as acidosis, glutamate excitotoxicity, calcium overload, cerebral inflammation and reactive oxygen species (ROS) generation. The current treatment for ischemic stroke is limited to thromolytics such as recombinant tissue plasminogen activator (tPA). tPA has a very narrow therapeutic window, making it suitable to only a minority of stroke patients. Hence, there is great urgency to develop new therapies that can protect brain tissue from ischemic damage. Recent studies have shown that new vessel formation after stroke not only replenishes blood flow to the ischemic area of the brain, but also promotes neurogenesis and improves neurological functions in both animal models and patients. Therefore, drugs that can promote angiogenesis after ischemic stroke can provide therapeutic benefits in stroke management. In this regard, Chinese herbal medicine (CHM) has a long history in treating stroke and the associated diseases. A number of studies have demonstrated the pro-angiogenic effects of various Chinese herbs and herbal formulations in both in vitro and in vivo settings. In this article, we present a comprehensive review of the current knowledge on angiogenesis in the context of ischemic stroke and discuss the potential use of CHM in stroke management through modulation of angiogenesis.
Transcanalicular diode laser-assisted dacryocystorhinostomy

Objective: We present a prospective, non-comparative case series study of 126 consecutive diode laser-assisted transcanalicular dacryocystorhinostomy (TCL-DCR) procedures on 122 patients. We analyzed success rate, procedure time and amount of laser energy needed for a 5 mm osteotomy. Materials and Methods: One hundred and twenty-two patients with nasolacrimal duct obstruction were included in the study. The procedure was performed under general anesthesia, and the nasal mucosa was anesthetized. An endoscope was used for examination of the lacrimal pathways. The site of osteotomy was determined with transillumination of the lateral nasal wall. We achieved osteotomy by applying laser energy via an optic fiber. We used a 980 nm diode laser with power of 10 Watts. We inserted a bicanalicular silicone stent as the last step. Success of procedure was absence of epiphora (subjective), or patency of the lacrimal drainage system on irrigation (objective). Results: We performed 126 successive endoscopic laser (EL-DCR) with bicanalicular intubation in 122 patients. The average procedure time was 12 min, and on average 245 Joules of laser energy was needed. The silicone stents were removed three to eight months after surgery. We observed absence of epiphora and a patent nasolacrimal duct on irrigation in 105 out of 126 treated eyes. Eighteen patients had epiphora despite a patent nasolacrimal duct on irrigation. This yields a success rate of 83.3%, with an average follow-up period of 12 months. Conclusions: The 980 nm EL-DCR with bicanalicular intubation is a new contribution to the field of lacrimal surgery. It is a minimally invasive quick procedure yielding a high success rate.