Miracle-dz/UniFAR-FTUs huggingface dataset:
Psychometric evidence of self-reported questionnaires for patellofemoral pain syndrome: a systematic review

Abstract Purpose: To conduct a systematic review of psychometric properties of self-reported questionnaires used to assess the level of symptoms and disability in individuals with patellofemoral pain syndrome (PFPS). Methods: A structured search was conducted in four databases (Medline, Embase, CINAHL, SportDiscus). A total of 24 studies about five different self-reported questionnaires were analyzed. A pair of independent raters extracted data on validity, reliability and responsiveness to change, and performed critical appraisal (0–100%). Results: Activities of Daily Living Scale (ADLS), Anterior Knee Pain Scale (AKPS), International Knee Documentation Committee (IKDC) and Lysholm Scale (LS) present excellent test–retest reliability (weighted average intraclass correlation coefficients [ICC] > 0.80), whereas Functional Index Questionnaire (FIQ) is moderately reliable (ICC = 0.61). Minimal detectable change is 8.3% for ADLS, 9.0% for AKPS, 19% for FIQ, 8.5% for IKDC and 30% for LS. ADLS, AKPS, IKDC and LS are highly responsive (effect size/standardized response mean >0.95) in individuals with PFPS, while FIQ is lowly responsive (effect size = 0.49). Conclusion: Based on available evidence, ADLS presents the best psychometric properties and should be preferred when evaluating patients with PFPS. AKPS and IKDC are also adequate, while FIQ and LS are not recommended for individuals with PFPS. Implications for Rehabilitation While several questionnaires have been developed to assess symptoms and functional limitations caused by knee pain, their psychometric properties can vary depending on the condition presented by the patient. The Activities of Daily Living Scale of the Knee Outcome Survey should be preferred by clinicians when evaluating a patient with PFPS. The Anterior Knee Pain Scale and International Knee Documentation Committee Subjective knee evaluation are also adequate for use with this population. The Functional Index Questionnaire and Lysholm Scale are not recommended for PFPS.
A matter of months: High precision migration chronology of a Bronze Age female

Establishing the age at which prehistoric individuals move away from their childhood residential location holds crucial information about the socio dynamics and mobility patterns in ancient societies. We present a novel combination of strontium isotope analyses performed on the over 3000 year old “Skrydstrup Woman” from Denmark, for whom we compiled a highly detailed month-scale model of her migration timeline. When combined with physical anthropological analyses this timeline can be related to the chronological age at which the residential location changed. We conducted a series of high-resolution strontium isotope analyses of hard and soft human tissues and combined these with anthropological investigations including CT-scanning and 3D visualizations. The Skrydstrup Woman lived during a pan-European period characterized by technical innovation and great social transformations stimulated by long-distance connections; consequently she represents an important part of both Danish and European prehistory. Our multidisciplinary study involves complementary biochemical, biomolecular and microscopy analyses of her scalp hair. Our results reveal that the Skrydstrup Woman was between 17–18 years old when she died, and that she moved from her place of origin -outside present day Denmark- to the Skrydstrup area in Denmark 47 to 42 months before she died. Hence, she was between 13 to 14 years old when she migrated to and resided in the area around Skrydstrup for the rest of her life. From an archaeological standpoint, this one-time and one-way movement of an elite female during the possible “age of marriageability” might suggest that she migrated with the aim of establishing an alliance between chiefdoms. Consequently, this detailed multidisciplinary investigation provides a novel tool to reconstruct high resolution chronology of individual mobility with the perspective of studying complex patterns of social and economic interaction in prehistory.
Ancient DNA, pig domestication, and the spread of the Neolithic into Europe

The Neolithic Revolution began 11,000 years ago in the Near East and preceded a westward migration into Europe of distinctive cultural groups and their agricultural economies, including domesticated animals and plants. Despite decades of research, no consensus has emerged about the extent of admixture between the indigenous and exotic populations or the degree to which the appearance of specific components of the “Neolithic cultural package” in Europe reflects truly independent development. Here, through the use of mitochondrial DNA from 323 modern and 221 ancient pig specimens sampled across western Eurasia, we demonstrate that domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic (potentially along two separate routes), reaching the Paris Basin by at least the early 4th millennium B.C. Local European wild boar were also domesticated by this time, possibly as a direct consequence of the introduction of Near Eastern domestic pigs. Once domesticated, European pigs rapidly replaced the introduced domestic pigs of Near Eastern origin throughout Europe. Domestic pigs formed a key component of the Neolithic Revolution, and this detailed genetic record of their origins reveals a complex set of interactions and processes during the spread of early farmers into Europe.
The impact of HIV infection on the presentation of lung cancer in South Africa.

BACKGROUND Despite the very high background prevalence of HIV and smoking-related diseases in sub-Saharan Africa, very little is known about the presentation of lung cancer in HIV-infected individuals. METHODS We prospectively compared HIV-positive (n=44) and HIV-negative lung cancer patients (n=425) with regard to demographics, cell type, performance status and umour node metastasis staging at initial presentation. RESULTS HIV-positive patients were found to be younger than HIV-negative (mean 54.1 (standard deviation (SD) 8.4) years v. 60.5 (10) years, p<0.01), more likely to have squamous cell carcinoma (43.2% v. 30.1%, p=0.07) and significantly more likely to have a poor Eastern Cooperative Oncology Group (ECOG) performance status of ≥3 (47.7% v. 29.4%, p=0.02). In the case of non-small cell-lung cancer, they were also significantly less likely to have early stage lung cancer (0% v. 10.3%, p=0.02) compared with HIV-negative patients. CONCLUSIONS HIV-positive lung cancer patients were younger, significantly more likely to have a poor performance status at presentation and significantly less likely to have early stage lung cancer when compared with HIV-negative patients.
Differences in UV transparency and thermal structure between alpine and subalpine lakes: implications for organisms

Ultraviolet (UV) radiation is a globally important abiotic factor influencing ecosystem structure and function in multiple ways. While UV radiation can be damaging to most organisms, several factors act to reduce UV exposure of organisms in aquatic ecosystems, the most important of which is dissolved organic carbon (DOC). In alpine lakes, very low concentrations of DOC and a thinner atmosphere lead to unusually high UV exposure levels. These high UV levels combine with low temperatures to provide a fundamentally different vertical structure to alpine lake ecosystems in comparison to most lowland lakes. Here, we discuss the importance of water temperature and UV transparency in structuring alpine lake ecosystems and the consequences for aquatic organisms that inhabit them. We present transparency data on a global data set of alpine lakes and nearby analogous subalpine lakes for comparison. We also present seasonal transparency data on a suite of alpine and subalpine lakes that demonstrate important differences in UV and photosynthetically active radiation (PAR, 400–700 nm) transparency patterns even within a single region. These data are used to explore factors regulating transparency in alpine lakes, to discuss implications of future environmental change on the structure and function of alpine lakes, and ways in which the UV transparency of these lakes can be used as a sentinel of environmental change.
General Formulation for the Analysis of Injection-Locked Coupled-Oscillator Systems

The use of an external injection-locking source prevents undesired frequency shifts in coupled-oscillator systems. Here an explicit formulation for the analysis of these systems is presented, based on a numerical model of the oscillator elements in free-running regime, obtained with harmonic balance. It demonstrates the opposed effects of oscillator coupling and injection locking in a realistic manner and brings to light the influence of the oscillator characteristics and coupling-network parameters. The explicit expressions provide the minimum injection-locking power required for a full variation of the inter-stage phase shift and enable the locking bandwidth to be fixed or maximized through a suitable choice of the coupling networks. Two different cases are considered: a basic system of three oscillator elements and a general system with any number of elements. In the latter case, the influence of the particular element chosen for the signal injection on the synchronization bandwidth is studied. The stability analysis is based on a perturbation system, which, unlike previous works, relies on a direct analytical calculation of the steady-state solutions, instead of a numerical one. This enables the full coverage of all possible solutions and hence an in-depth understanding of the influence of the coupling network and injection source on the stable phase-shift ranges. The phase noise analysis, applied to the same explicit formulation, demonstrates the injection locking effects and enables the identification of different regions as the offset frequency increases.
The value of laparoscopic staging for patients with colorectal metastases.

BACKGROUND Resection offers the only chance of cure for hepatic colorectal metastases. However, preoperative staging does not always reliably detect unresectable disease. The aim of this study was to investigate the role that laparoscopy with ultrasound may have in detecting unresectable disease, thus sparing patients from unnecessary laparotomy with the associated morbidity and cost. METHODS A retrospective review of all patients considered for liver resection of colorectal metastases during a 3-year period was performed, analyzing factors likely to predict resectable disease, rates of resectability, and success of laparoscopic staging at detecting unresectable disease. RESULTS Of 73 patients with resectable disease on computed tomography, 24 were deemed to need laparoscopy, and 49 proceeded directly to laparotomy. Those first undergoing laparoscopy had shorter disease-free intervals between diagnosis of colorectal cancer and detection of hepatic recurrence and greater numbers of hepatic metastases. Twelve of the 24 patients who underwent laparoscopy had unresectable disease, and 8 of these were detected at laparoscopy. Forty-six of the 49 patients proceeding to laparotomy directly had resectable disease. CONCLUSIONS Laparoscopic staging of hepatic colorectal metastatic disease detects most unresectable disease, preventing unnecessary laparotomy. The likelihood of disease being unresectable is in part predicted by the disease-free interval and the number of hepatic metastases.
Carotid Plaque Calcification Predicts Future Cardiovascular Events in Type 2 Diabetes

OBJECTIVE The presence of carotid plaques is associated with future cardiovascular events, with local plaque composition being an independent outcome predictor. We examined the association between ultrasonographically determined carotid plaque calcification and incident major adverse cardiovascular events (MACE) and death in type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS We enrolled 581 patients with T2D who underwent routine carotid ultrasonography. Plaques were classified as echolucent (lipid rich), heterogenous, and echogenic (calcific). We collected demographic, anthropometric, and clinical data at baseline and followed the patients for up to 9 years. RESULTS Plaques were detected in 81.8% of the patients (echolucent in 16.4%, heterogenous in 43.2%, and echogenic in 22.2%). During follow-up (4.3 ± 0.1 years), 58 deaths (27 cardiovascular) and 236 fatal and nonfatal MACE occurred. In univariate analyses, presence versus absence of any carotid plaque was associated with incident MACE, and the hazard ratio (95% CI) progressively increased from echolucent (1.97 [0.93–3.44]), to heterogeneous (3.10 [2.09–4.23]), to echogenic (3.71 [2.09–5.59]) plaques. Compared with echolucent plaques, echogenic plaques were associated with incident MACE independently from confounders. This association was attenuated after adjusting for the degree of stenosis, but in patients with stenosis ≤30%, echogenic plaque type still predicted total and atherosclerotic MACE, even after further adjusting for mean intima-media thickness. CONCLUSIONS In T2D, carotid plaque calcification predicts MACE, especially in patients with a low degree of stenosis. The biology of atherosclerotic calcification in diabetes needs to be further elucidated to understand the basis of this association.
Reflections on macroeconometric modeling

Abstract I have been doing research in macroeconomics since the late 1960s, almost 50 years. In this paper I pause and take stock. The paper is part personal reflections on macroeconometric modeling, part a road map of the techniques of macroeconometric modeling, and part comments on what I think I have learned about how the macroeconomy works from my research in this area. Section 1 contrasts the methodology of the Cowles Commission approach with that of DSGE modeling. Section 2 presents the general model that I am using; Section 3 discusses theory; and Section 4 discusses estimation and solution. Section 5 then discusses various results from the estimation; Section 6 discusses various properties of the model; and Section 7 uses the model to analyze various economic events. Wealth effects play a large role in the analysis of past events.
A Qualitative Study of Barriers to Enrollment into Free HIV Care: Perspectives of Never-in-Care HIV-Positive Patients and Providers in Rakai, Uganda

Background. Early entry into HIV care is low in Sub-Saharan Africa. In Rakai, about a third (31.5%) of HIV-positive clients who knew their serostatus did not enroll into free care services. This qualitative study explored barriers to entry into care from HIV-positive clients who had never enrolled in care and HIV care providers. Methods. We conducted 48 in-depth interviews among HIV-infected individuals aged 15–49 years, who had not entered care within six months of result receipt and referral for free care. Key-informant interviews were conducted with 12 providers. Interviews were audio-recorded and transcripts subjected to thematic content analysis based on the health belief model. Results. Barriers to using HIV care included fear of stigma and HIV disclosure, women's lack of support from male partners, demanding work schedules, and high transport costs. Programmatic barriers included fear of antiretroviral drug side effects, long waiting and travel times, and inadequate staff respect for patients. Denial of HIV status, belief in spiritual healing, and absence of AIDS symptoms were also barriers. Conclusion. Targeted interventions to combat stigma, strengthen couple counseling and health education programs, address gender inequalities, and implement patient-friendly and flexible clinic service hours are needed to address barriers to HIV care.
The Effect of Intravitreal Ranibizumab on the Fellow Untreated Eye with Subfoveal Scarring due to Exudative Age-Related Macular Degeneration

Aim: Our purpose was to evaluate the possible effect of intravitreal ranibizumab on the fellow untreated eye with choroidal neovascularization (CNV) and subfoveal scarring associated with age-related macular degeneration (AMD). Methods: A retrospective observational study was conducted. One hundred eighty-seven ranibizumab-treated patients diagnosed as having subfoveal CNV scarring in the untreated eye were compared with a control group of untreated unilateral subfoveal CNV scarring. Inclusion criteria concerning treated eyes in the ranibizumab group complied with the MARINA and ANCHOR studies. Demographic data, clinical course, visual acuity, fluorescein angiography and optical coherence tomography findings were evaluated. Results: Clinical improvement was confirmed in 24% of the patients in the ranibizumab group and in only 12.9% of the controls. Improvement was noted as early as 2–4 months (2.83 ± 0.75 months) after the initiation of treatment in the fellow eye compared with 33.25 ± 9.43 months in the control group (p = 0.01; Mann-Whitney U test). Kaplan-Meier curves demonstrate the positive impact of ranibizumab on the visual acuity of the fellow untreated eye (p = 0.016; Log-Rank test). Conclusions: Ranibizumab might induce some therapeutic effect in selected cases of end-stage CNV scarring, which needs to be further examined. The VEGF levels in the compartments of the fellow eye of patients with age-related macular degeneration treated with ranibizumab need to be further evaluated.
Molecular Systems Biology Peer Review Process File Common Dysregulation Network in the Human Prefrontal Cortex Underlies Two Neurodegenerative Diseases Transaction Report

(Note: With the exception of the correction of typographical or spelling errors that could be a source of ambiguity, letters and reports are not edited. The original formatting of letters and referee reports may not be reflected in this compilation.) Thank you again for submitting your work to Molecular Systems Biology. We have now heard back from two of the three reviewers who agreed to evaluate your manuscript. As you will see from the reports below, the referees raise substantial concerns on your work, which, I am afraid to say, preclude its publication in Molecular Systems Biology. Both reviewers acknowledged the substantial amount of new data presented in this work; however, both independently indicated that were not convinced that this work offered the kind of depth of biological insight or conclusiveness that would be expected in Molecular Systems Biology. The reviewers found the novel conceptual insights into the molecular systems specifically underlying Alzheimer's or Huntington's disease to be modest, and indicated that these data deserved deeper functional investigation and more rigorous validation. In addition, both reviewers had clear concerns regarding the conclusiveness of the mouse model expression profiling results. The second reviewer also raised important technical concerns regarding the statistical analyses, which s/he felt were sufficient to case doubt on some of the results of this study. Given these concerns, and the low-level of support from the reviewers, I see no other choice than to return the manuscript with the message that we cannot offer to publish it.
Biogeographic and bathymetric determinants of brachiopod extinction and survival during the Late Ordovician mass extinction

The Late Ordovician mass extinction (LOME) coincided with dramatic climate changes, but there are numerous ways in which these changes could have driven marine extinctions. We use a palaeobiogeographic database of rhynchonelliform brachiopods to examine the selectivity of Late Ordovician–Early Silurian genus extinctions and evaluate which extinction drivers are best supported by the data. The first (latest Katian) pulse of the LOME preferentially affected genera restricted to deeper waters or to relatively narrow (less than 35°) palaeolatitudinal ranges. This pattern is only observed in the latest Katian, suggesting that it reflects drivers unique to this interval. Extinction of exclusively deeper-water genera implies that changes in water mass properties such as dissolved oxygen content played an important role. Extinction of genera with narrow latitudinal ranges suggests that interactions between shifting climate zones and palaeobiogeography may also have been important. We test the latter hypothesis by estimating whether each genus would have been able to track habitats within its thermal tolerance range during the greenhouse–icehouse climate transition. Models including these estimates are favoured over alternative models. We argue that the LOME, long regarded as non-selective, is highly selective along biogeographic and bathymetric axes that are not closely correlated with taxonomic identity.
Identification and functional characterization of two novel NPR2 mutations in Japanese patients with short stature.

CONTEXT C-type natriuretic peptide-natriuretic peptide receptor B (NPR-B) signaling is critical for endochondral ossification, which is responsible for longitudinal growth in limbs and vertebrae. Biallelic NPR2 mutations cause acromesomelic dysplasia, type Maroteaux, which is bone dysplasia characterized by severe short stature and short limbs. A monoallelic NPR2 mutation has been suggested to mildly impair long bone growth. OBJECTIVE The goal of this study was to identify and characterize NPR2 mutations among Japanese patients with short stature. SUBJECTS AND METHODS We enrolled 101 unrelated Japanese patients with short stature. NPR2 and NPPC were sequenced, and the identified variants were characterized in vitro. RESULTS In two subjects, we identified two novel heterozygous NPR2 mutations (R110C and Q417E) causing a loss of C-type natriuretic peptide-dependent cGMP generation capacities and having dominant-negative effects. R110C was defective in trafficking from the endoplasmic reticulum to the Golgi apparatus. In contrast, Q417E showed clear cell surface expression. CONCLUSIONS We identified heterozygous NPR2 mutations in 2% of Japanese patients with short stature. Our in vitro findings indicate that NPR2 mutations have a dominant negative effect, and their dominant-negative mechanisms vary corresponding to the molecular pathogenesis of the mutations.
Guaranteeing Performance Yield in High-Level Synthesis

Meeting timing constraint is one of the most important issues for modern design automation tools. This situation is exacerbated with the existence of process variation. Current high-level synthesis tools, performing task scheduling, resource allocation and binding, may result in unexpected performance discrepancy due to the ignorance of the impact of process variation, which requires a shift in the design paradigm, from today's deterministic design to statistical or probabilistic design. In this paper, we present a variation-aware performance yield-guaranteed high-level synthesis algorithm. The proposed approach integrates high-level synthesis and statistical static timing analysis into a simulated annealing engine to simultaneously explore solution space while meeting design objectives. Our results show that the area reduction is in the average of 14% when 95% performance yield is imposed with the same total completion time constraint
The MusES system: an environment for experimenting with knowledge representation techniques in tonal harmony

We report here on current works on the MusES environment, designed for experimenting with various objectoriented knowledge representation techniques in the field of tonal harmony. The first layer of MusES is a repository of consensus knowledge about tonal harmony, including an explicit representation of enharmonic spelling, as well as representation of intervals, scales and chords that support standard computations. We give an overview of several systems built on top of MusES: a system for the analysis of jazz chord sequences, a system for the automatic generation of harmonizations, and a system that generates real-time jazz improvisations. We give an overview of MusES and its extensions and discuss several representation issues and their solutions in MusES.