Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic verification of correspondences for security protocols

We present a new technique for verifying correspondences in security protocols. In particular, correspondences can be used to formalize authentication. Our technique is fully automatic, it can handle an unbounded number of sessions of the protocol, and it is efficient in practice. It significantly extends a previous technique for the verification of secrecy. The protocol is represented in an extension of the pi calculus with fairly arbitrary cryptographic primitives. This protocol representation includes the specification of the correspondence to be verified, but no other annotation. This representation is then translated into an abstract representation by Horn clauses, which is used to prove the desired correspondence. Our technique has been proved correct and implemented. We have tested it on various protocols from the literature. The experimental results show that these protocols can be verified by our technique in less than 1 s.
Challenges in Supporting Survivors of Child Sexual Abuse in Kenya: A Qualitative Study of Government and Non-governmental Organizations

Child sexual abuse (CSA) is a global, social, and health challenge. Existing literature on post-sexual assault care has focused largely on health providers’ skills and capacity to offer quality clinical, medicolegal, and psychosocial care. Services other than medical and psychosocial care provided to survivors of CSA remain poorly studied, particularly in the global south. The study aimed to explore challenges facing service providers supporting children who have experienced sexual abuse and make suitable recommendations. We triangulated different qualitative methods: in-depth interviews with 61 key informants, three focus group discussions with community leaders, and unstructured observations for data collection. Findings indicate that service providers supporting children who had experienced sexual abuse play a vital role in ensuring that survivors receive clinical and medicolegal care, psychosocial support, have access to justice, and are protected from further victimization. However, these service providers face several challenges, including poor infrastructure, the lack of effective coordination and linkage among the service providers in the continuum of care, corruption among officials, and harmful patriarchal norms that hinder reporting of abuse. To effectively support and care for survivors, we recommend government commitment to, and investments in, safe spaces, supervision, and professional development of providers. Working with community leaders and gatekeepers of all genders is critical to address harmful practices that perpetuate CSA and make it difficult to care for and obtain justice for CSA survivors.
Characteristics of Treatment Naïve Chronic Hepatitis B in Bangladesh: Younger Populations are More Affected; HBeAg-negatives are More Advanced

Background/Aim: Bangladesh is a densely populated country with intermediate endemicity for chronic hepatitis B (CHB). The aim of the present study was to evaluate the biochemical, virological and histological character of CHB patients and to examine the relationship between these indices. Materials and Methods: One thousand and twenty-two patients of CHB fulfilled our inclusion criteria. Inclusion criteria were (1) HBsAg positive for at least 6 months, (2) HBeAg-positive or negative and (3) hepatitis B virus (HBV) DNA positive. Patients with detectable antibodies to human immunodeficiency virus (HIV), hepatitis Delta virus (HDV) or hepatitis C virus (HCV), with previous antiviral treatment, overt cirrhosis and hepatocellular carcinoma, were excluded. Of these, 191 patients were randomly selected for liver biopsy and were evaluated for analysis. Results: In the 191 patients, male to female ratio was 4.6:1; age distribution was 26.5 ± 8.5 (mean ± standard deviation) years. One hundred and seventy-eight (93.2%) patients were under 40 years. Sixty-eight (35.6%) patients were HBeAg-negative, had less DNA load, and were significantly older, more fibrotic and cirrhotic (P < 0.001). Correlation was not found between DNA level and histological activity. Histological activity was not correlated with ALT level in HBeAg-positive patients (P < 0.001). Conclusion: CHB affects the younger population in Bangladesh. HBeAg-positive CHB was associated with more fibrosis and cirrhosis. Serum HBV DNA levels do not correlate with the severity of histological lesions in all patients. Evaluation by liver biopsy remains gold standard for taking decision of treatment.
Adjacent segment disease after posterior lumbar instrumentation surgery for degenerative disease: Incidence and risk factors

Purpose: To identify risk factors for occurrence of symptomatic adjacent segment disease (ASD) after posterior lumbar instrumentation surgery. Methods: This retrospective study evaluated 630 patients who underwent posterior lumbar transpedicular instrumentation for degenerative lumbar disorders between April 2008 and April 2012. On the basis of developing ASD at follow-up, patients were categorized into two groups: the ASD group and the non-ASD (N-ASD) group. These two groups were compared for patient characteristics, surgical variables, and radiographic parameters to investigate the possible predictive factors of ASD. Results: Of the 630 individuals participated in the study, 76 (12.1%) patients had ASD. Mean and standard deviation of age were 61.37 ± 4.12 years for the ASD group and 62.37 ± 3.9 for the N-ASD group (p = 0.79). The average follow-up period was 51 ± 2.2 months in the ASD group and 52 ± 2.3 months in the N-ASD group (p = 0.691). There were no significant differences between the two groups in terms of gender, diabetes mellitus (DM), hypertension, smoking, and osteoporosis, with all p > 0.05. The logistic regression analysis demonstrated that higher preoperative body mass index (BMI; odds ratio (OR) 1.233, p = 0.005), preoperative disc degeneration (OR 1.033, p = 0.024), decreased postoperative lumbar lordosis (OR 3.080, p = 0.011), fusion at more than four levels (OR 4.280, p = 0.014), and intraoperative superior facet joint violation (OR 7.480, p = 0.009) were independently associated with ASD. Conclusions: Patients with higher preoperative BMI, preoperative disc degeneration, decreased postoperative lumbar lordosis, fusion at more than four levels, and intraoperative superior facet joint violation have a statistically significant increased risk of developing ASD.
Potential Interactions of Biologically Based Complementary Medicine in Gynecological Oncology

Objective. The aim of this study was to assess the potential risks of interactions between biologically based complementary and alternative medication (BB-CAM) and conventional drugs during systemic therapy in breast and gynecological cancer patients by analyzing the actual CAM-drug combinations from individual patients’ records. Methods. From September 2014 to December 2014 and from February 2017 to May 2017, all patients (n = 717) undergoing systemic therapy at the Gynecologic Oncology Day Care Unit in the Gynecology and Obstetrics Department of the Technical University of Munich, Germany, were asked to participate in a questionnaire about all their medications. To assess the potential risk of CAM-drug interactions (CDIs), we initially utilized the Lexicomp drug interaction database. This assessment was then expanded with a systematic search of other digital databases, such as the National Center for Complementary and Integrative Health, Memorial Sloan Kettering Cancer Center, PubMed, and MEDLINE as well as the Cochrane Library. Results. Among 448 respondents, 74.1% reported using BB-CAM simultaneously with their systemic therapy. The assessment showed 1 patient with a potentially clinically relevant CDI, where the interaction was based on a self-medicated combination of Echinacea and cyclophosphamide. Furthermore, 81 patients (18.1%) were thought to have interactions because of a combination of BB-CAMs and cytochrome P450 3A4–metabolized anticancer drugs. Conclusions. Our data demonstrated high overall use of BB-CAMs by cancer patients undergoing systemic therapy. The analyses showed only 1 clinically relevant CDI.
Immunocytochemistry for predictive biomarker testing in lung cancer cytology

With an escalating number of predictive biomarkers emerging in non–small cell lung carcinoma (NSCLC), immunohistochemistry (IHC) is being used as a rapid and cost‐effective tool for the screening and detection of many of these markers. In particular, robust IHC assays performed on formalin‐fixed, paraffin‐embedded (FFPE) tumor tissue are widely used as surrogate markers for ALK and ROS1 rearrangements and for detecting programmed death ligand 1 (PD‐L1) expression in patients with advanced NSCLC; in addition, they have become essential for treatment decisions. Cytology samples represent the only source of tumor in a significant proportion of patients with inoperable NSCLC, and there is increasing demand for predictive biomarker testing on them. However, the wide variation in the types of cytology samples and their preparatory methods, the use of alcohol‐based fixatives that interfere with immunochemistry results, the difficulty in procurement of cytology‐specific controls, and the uncertainty regarding test validity have resulted in underutilization of cytology material for predictive immunocytochemistry (ICC), and most cytopathologists limit such testing to FFPE cell blocks (CBs). The purpose of this review is to: 1) analyze various preanalytical, analytical, and postanalytical factors influencing ICC results; 2) discuss measures for validation of ICC protocols; and 3) summarize published data on predictive ICC for ALK, ROS1, EGFR gene alterations and PD‐L1 expression on lung cancer cytology. Based on our experience and from a review of the literature, we conclude that cytology specimens are in principal suitable for predictive ICC, but proper optimization and rigorous quality control for high‐quality staining are essential, particularly for non‐CB preparations.
Arrhythmic risk stratification in post-myocardial infarction patients with preserved ejection fraction: the PRESERVE EF study

Abstract Aims Sudden cardiac death (SCD) annual incidence is 0.6–1% in post-myocardial infarction (MI) patients with left ventricular ejection fraction (LVEF)≥40%. No recommendations for implantable cardioverter-defibrillator (ICD) use exist in this population. Methods and results We introduced a combined non-invasive/invasive risk stratification approach in post-MI ischaemia-free patients, with LVEF ≥ 40%, in a multicentre, prospective, observational cohort study. Patients with at least one positive electrocardiographic non-invasive risk factor (NIRF): premature ventricular complexes, non-sustained ventricular tachycardia, late potentials, prolonged QTc, increased T-wave alternans, reduced heart rate variability, abnormal deceleration capacity with abnormal turbulence, were referred for programmed ventricular stimulation (PVS), with ICDs offered to those inducible. The primary endpoint was the occurrence of a major arrhythmic event (MAE), namely sustained ventricular tachycardia/fibrillation, appropriate ICD activation or SCD. We screened and included 575 consecutive patients (mean age 57 years, LVEF 50.8%). Of them, 204 (35.5%) had at least one positive NIRF. Forty-one of 152 patients undergoing PVS (27–7.1% of total sample) were inducible. Thirty-seven (90.2%) of them received an ICD. Mean follow-up was 32 months and no SCDs were observed, while 9 ICDs (1.57% of total screened population) were appropriately activated. None patient without NIRFs or with NIRFs but negative PVS met the primary endpoint. The algorithm yielded the following: sensitivity 100%, specificity 93.8%, positive predictive value 22%, and negative predictive value 100%. Conclusion The two-step approach of the PRESERVE EF study detects a subpopulation of post-MI patients with preserved LVEF at risk for MAEs that can be effectively addressed with an ICD. Clinicaltrials.gov identifier NCT02124018
Well Water in Karst Regions of Northeastern Wisconsin Contains Estrogenic Factors, Nitrate, and Bacteria

Well water in karst regions is particularly susceptible to contamination by various nonpoint source pollutants such as nitrate, fecal bacteria, and endocrine disrupting chemicals (EDCs). This study analyzed 40 wells in heavily farmed karst areas of northeastern Wisconsin to determine whether these and other pollutants are present, and if so, whether their presence is (1) correlated with other contaminants and (2) exhibits seasonal variation. Nitrate, bacteria, and estrogenicity (indicating the presence of EDCs) were present in at least some of well water samples collected over the course of four time periods between the summers of 2008 and 2009. Although estrogenicity was greatest during the summer months, bacterial contamination was most prevalent during snowmelt. Levels of estrogenicity present in some well water samples approached a threshold concentration that is known to exert endocrine disruption in wildlife. Strong correlations between estrogenicity and other water quality parameters were not found.
Patient perspectives on the process and outcomes of psychiatric genetic counseling: An “Empowering Encounter”

Genetic counseling (GC) for individuals with mental illness (MI) has been shown to improve patient outcomes, such as increased empowerment and self‐efficacy. However, we do not understand how the process of GC results in these improvements or what aspects of the process are critical. In this qualitative study, we explored the process and outcome of psychiatric GC from the patient's perspective. Ten Canadian adults with a diagnosed MI were interviewed prior to, and 1 month following, psychiatric GC. Interview transcripts were analyzed using Grounded Theory methodology and generated a theoretical framework that describes the process and outcomes of psychiatric GC from the patient's perspective. Participants described the counseling process to be an “empowering encounter” and identified specific attributes of the process and characteristics of the counselor that contributed to their empowerment. Participants gained a new perspective on the cause and management of their MI, which seemed to facilitate a deeper acceptance of their condition. Consequently, participants reported being empowered and feeling less shame, blame, and guilt; which reportedly made them more able to manage their MI and protect their mental health; and more open to talking about their condition with family and friends. This study provides a better understanding of how the process of GC influences patient outcomes and highlights features of the process that maximize patient benefit.
Predicting Wellness After Pediatric Concussion

Abstract Objective: Concussion in children and adolescents is a prevalent problem with implications for subsequent physical, cognitive, behavioral, and psychological functioning, as well as quality of life. While these consequences warrant attention, most concussed children recover well. This study aimed to determine what pre-injury, demographic, and injury-related factors are associated with optimal outcome (“wellness”) after pediatric concussion. Method: A total of 311 children 6–18 years of age with concussion participated in a longitudinal, prospective cohort study. Pre-morbid conditions and acute injury variables, including post-concussive symptoms (PCS) and cognitive screening (Standardized Assessment of Concussion, SAC), were collected in the emergency department, and a neuropsychological assessment was performed at 4 and 12 weeks post-injury. Wellness, defined by the absence of PCS and cognitive inefficiency and the presence of good quality of life, was the main outcome. Stepwise logistic regression was performed using 19 predictor variables. Results: 41.5% and 52.2% of participants were classified as being well at 4 and 12 weeks post-injury, respectively. The final model indicated that children who were younger, who sustained sports/recreational injuries (vs. other types), who did not have a history of developmental problems, and who had better acute working memory (SAC concentration score) were significantly more likely to be well. Conclusions: Determining the variables associated with wellness after pediatric concussion has the potential to clarify which children are likely to show optimal recovery. Future work focusing on wellness and concussion should include appropriate control groups and document more extensively pre-injury and injury-related factors that could additionally contribute to wellness. (JINS, 2019, 25, 375–389)
Behavior of geodesic-length functions on Teichmüller space

Let T be the Teichmuller space of marked genus g, n punctured Riemann surfaces with its bordification T the augmented Teichmuller space of marked Riemann surfaces with nodes, (Abi77, Ber74). Pro- vided with the WP metric T is a complete CAT(0) metric space, (DW03, Wol03, Yam04). An invariant of a marked hyperbolic struc- ture is the lengthof the geodesic in a free homotopy class. A basic feature of Teichmuller theory is the interplay of two-dimensional hyperbolic geometry, Weil-Petersson (WP) geometry and the behavior of geodesic-length functions. Our goal is to develop the understanding of the intrinsic local WP geometry through a study of the gradient and Hessian of geodesic-length functions. Considerations include ex- pansions for the WP pairing of gradients, expansions for the Hessian and covariant derivative, comparability models for the WP metric, as well as the behavior of WP geodesics including a description of the Alexandrov tangent cone at the augmentation. Approximations and applications for geodesics close to the augmentation are developed. An application for fixed points of group actions is described. Bound- ing configurations and functions on the hyperbolic plane is basic to our approach. Considerations include analyzing the orbit of a dis- crete group of isometries and bounding sums of the inverse square exponential-distance.
Primäre Rekonstruktion der ableitenden Tränenwege nach Trauma – bikanalikulonasale Schienung mit autostabilen Silikonverweilsonden

Zusammenfassung Verletzungen des medialen Lidwinkels können alle Abschnitte der ableitenden Tränenwege (TNW) involvieren. Je nach Alter der Patienten finden sich typische Verletzungsmuster. Die chirurgische Tränenwegsrekonstruktion durch 2 autostabile („selbsthaltende“) monokanalikulonasale Silikonverweilsonden soll anhand von 2 Fallberichten beschrieben werden. Ein 6 Jahre altes Mädchen zeigte infolge eines Hundebisses (Rottweiler) neben schwerwiegenden Kopfverletzungen eine tiefe periokuläre Weichteilwunde mit Tränenwegsbeteiligung. Der Canaliculus lacrimalis inferior war durchtrennt und der Canaliculus lacrimalis communis war vom Tränensack abgerissen. Schwerste Weichteilverletzungen ausgehend vom Unterlid erstreckten sich bis zur Wange und Nase. Mittels nahtfixierten monokanalikulonasalen Silikonverweilsonden und Kanalikulusnähten sowie einer schichtweisen Weichteilrekonstruktion wurden die TNW und das Lid rekonstruiert. 18 Monate postoperativ zeigt sich eine diskrete Depression der medialen Unterlidkante bei sonst guter Funktion. Der 2. Fall berichtet von einem 43 Jahre alten Fleischereifachangestellten, der sich mit einem Messer eine tiefe Wunde des medialen Lidwinkels zuzog. Bei dem erwachsenen Patienten waren beide Tränenröhrchen weit proximal (sakkusnah) sowie das mediale Lidbändchen und der M. orbicularis oculi durchtrennt. Nach Einbringen zweier monokanalikulonasaler Silikonverweilsonden wurde eine mikrochirurgische Rekonstruktion vorgenommen. Das Follow-up bei diesem Patienten beträgt 6 Monate. Klinisch und funktionell bestand abschließend bei beiden Patienten kein Anhalt für eine Tränenabflussstörung. Zeitgleich können mehrere Abschnitte der TNW verletzt sein. Das Erkennen und das korrekte Zuordnen des Verletzungsmusters in Hinblick auf Schädigungsart, -grad und die anatomische Lokalisation sind grundlegend für eine adäquate Rekonstruktion der TNW. Ein schichtweiser Wundverschluss von innen nach außen unter Berücksichtigung der topografischen Anatomie ist obligat. Die Wiederherstellung der funktionellen Einheit von Lidern und TNW ist hierbei anzustreben. Autostabile monokanalikulonasale Silikonverweilsonden können nach Trauma zur Schienung beider Tränenröhrchen sowohl bei Kindern als auch Erwachsenen zur Anwendung kommen.
Accounting for masking of frequency modulation by amplitude modulation with the modulation filter-bank concept.

Frequency modulation (FM) is assumed to be detected through amplitude modulation (AM) created by cochlear filtering for modulation rates above 10 Hz and carrier frequencies (fc) above 4 kHz. If this is the case, a model of modulation perception based on the concept of AM filters should predict masking effects between AM and FM. To test this, masking effects of sinusoidal AM on sinusoidal FM detection thresholds were assessed on normal-hearing listeners as a function of FM rate, fc, duration, AM rate, AM depth, and phase difference between FM and AM. The data were compared to predictions of a computational model implementing an AM filter-bank. Consistent with model predictions, AM masked FM with some AM-masking-AM features (broad tuning and effect of AM-masker depth). Similar masking was predicted and observed at fc = 0.5 and 5 kHz for a 2 Hz AM masker, inconsistent with the notion that additional (e.g., temporal fine-structure) cues drive slow-rate FM detection at low fc. However, masking was lower than predicted and, unlike model predictions, did not show beating or phase effects. Broadly, the modulation filter-bank concept successfully explained some AM-masking-FM effects, but could not give a complete account of both AM and FM detection.
Role for RNA:DNA hybrids in origin-independent replication priming in a eukaryotic system

Significance R-loop formation has been related to genome instability and human disease, yet the role of R-loops in replication priming remains to be explored in the eukaryotic genome. This investigation discloses that transcription-dependent R-loops have the potential to initiate origin-independent replication events in ribosomal DNA. Taken together, our data suggest that R-loops contribute to transcription-driven endoreplication events and alterations in genome copy number. DNA replication initiates at defined replication origins along eukaryotic chromosomes, ensuring complete genome duplication within a single S-phase. A key feature of replication origins is their ability to control the onset of DNA synthesis mediated by DNA polymerase-α and its intrinsic RNA primase activity. Here, we describe a novel origin-independent replication process that is mediated by transcription. RNA polymerase I transcription constraints lead to persistent RNA:DNA hybrids (R-loops) that prime replication in the ribosomal DNA locus. Our results suggest that eukaryotic genomes have developed tools to prevent R-loop–mediated replication events that potentially contribute to copy number variation, particularly relevant to carcinogenesis.