Best practices to evaluate the impact of biomedical research software-metric collection beyond citations.

MOTIVATION: Software is vital for the advancement of biology and medicine. Impact evaluations of scientific software have primarily emphasized traditional citation metrics of associated papers, despite these metrics inadequately capturing the dynamic picture of impact and despite challenges with improper citation. RESULTS: To understand how software developers evaluate their tools, we conducted a survey of participants in the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We found that although developers realize the value of more extensive metric collection, they find a lack of funding and time hindering. We also investigated software among this community for how often infrastructure that supports more nontraditional metrics were implemented and how this impacted rates of papers describing usage of the software. We found that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seemed to be associated with increased mention rates. Analysing more diverse metrics can enable developers to better understand user engagement, justify continued funding, identify novel use cases, pinpoint improvement areas, and ultimately amplify their software's impact. Challenges are associated, including distorted or misleading metrics, as well as ethical and security concerns. More attention to nuances involved in capturing impact across the spectrum of biomedical software is needed. For funders and developers, we outline guidance based on experience from our community. By considering how we evaluate software, we can empower developers to create tools that more effectively accelerate biological and medical research progress. AVAILABILITY AND IMPLEMENTATION: More information about the analysis, as well as access to data and code is available at https://github.com/fhdsl/ITCR_Metrics_manuscript_website.

Clinical value of neuroimaging indicators of intracranial hypertension in patients with cerebral venous thrombosis.

PURPOSE: Intracranial hypertension (IH) frequently complicates cerebral venous thrombosis (CVT). Distinct neuroimaging findings are associated with IH, yet their discriminative power, reversibility and factors favoring normalization in prospective CVT patients are unknown. We determined test performance measures of neuroimaging signs in acute CVT patients, their longitudinal change under anticoagulation, association with IH at baseline and with recanalization at follow-up. METHODS: We included 26 consecutive acute CVT patients and 26 healthy controls. Patients were classified as having IH based on CSF pressure > 25 cmH2O and/or papilledema on ophthalmological examination or ocular MRI. We assessed optic nerve sheath diameter (ONSD), optic nerve tortuousity, bulbar flattening, lateral and IVth ventricle size, pituitary configuration at baseline and follow-up, and their association with IH and venous recanalization. RESULTS: 46% of CVT patients had IH. ONSD enlargement > 5.8 mm, optic nerve tortuousity and pituitary grade ≥ III had highest sensitivity, ocular bulb flattening and pituitary grade ≥ III highest specificity for IH. Only ONSD reliably discriminated IH at baseline. Recanalization was significantly associated with regressive ONSD and pituitary grade. Other neuroimaging signs tended to regress with recanalization. After treatment, 184.9 ± 44.7 days after diagnosis, bulbar flattening resolved, whereas compared with controls ONSD enlargement (p < 0.001) and partially empty sella (p = 0.017), among other indicators, persisted. CONCLUSION: ONSD and pituitary grading have a high diagnostic value in diagnosing and monitoring CVT-associated IH. Given their limited sensitivity during early CVT and potentially persistent alterations following IH, neuroimaging indicators can neither replace CSF pressure measurement in diagnosing IH, nor determine the duration of anticoagulation.

The Consolidation of Risk Pools in the National Health Insurance Program of the Republic of Korea: Analysis of the Political Processes.

South Korea is one of the few countries that has successfully consolidated its national risk pools into a single-payer health insurance system. This study analyzes national health insurance (NHI) consolidation in South Korea between 1980 and 2003, drawing lessons for countries seeking to consolidate their risk pools. The paper contextualizes the development of the South Korean national health insurance system and the consolidation of its risk pools in the changes in the political environment, particularly the processes of political democratization. It examines how these processes have affected the societal meanings and roles of the health insurance system. The paper focuses on two policy stages. During the agenda-setting stage, the government and employers emphasized the efficiency of the health insurance system. This emphasis contributed to the failure of a consolidation plan that emphasized equity over efficiency. However, as democratization expanded, the power of civil society movements and the popular demand for equity grew stronger. During the policy adoption phase, consolidation of health insurance trusts in South Korea was achieved through social and political processes that influenced public opinion, expanded civil society participation in decision-making, and worked with the government to integrate health insurance organizations and funds.

Reassessing Trabeculectomy: A Long-Term Study with Stringent Success Criteria.

Background: The aim was to evaluate the long-term outcome and efficacy of primary trabeculectomy with adjunctive mitomycin c (MMC) for treating glaucoma. Methods: We examined the medical records of 286 eyes that underwent trabeculectomy between 2008 and 2009 at the University Eye Hospital in Freiburg, Germany. Preoperative and follow-up data were collected, including intraocular pressure (IOP) measurements, surgical glaucoma interventions, and prescribed glaucoma medication. The first success criterion was defined as IOP ≤ 15 mmHg with no use of pressure-lowering medication by the patient, the second criterion was defined as the absence of surgical revision, and the third criterion as no further IOP-lowering surgery excluding early revisions following trabeculectomy. Statistical analyses comprised Cox regression and Kaplan-Meier survival estimations. Results: The mean follow-up duration was 1841 days (5 years). The mean preoperative IOP was 26.1 mmHg. Evaluating the success criteria at the time of average follow-up yielded a success rate of only 25% for the first criterion but 80% for both the second and third success criteria. Conclusions: The findings suggest that trabeculectomy with adjunctive MMC can be an effective procedure for permanently lowering IOP. However, surgical revisions and/or further glaucoma surgeries might still be needed. The long-term success rate is lower in comparison to previous research, which may be explained by the stricter success criteria in our study.

Detection and validation of common noctule bats (Nyctalus noctula) with a pulse radar and acoustic monitoring in the proximity of an onshore wind turbine.

This paper presents the results of bats detected with marine radar and their validation with acoustic detectors in the vicinity of a wind turbine with a hub height of 120 m. Bat detectors are widely used by researchers, even though the common acoustic detectors can cover only a relatively small volume. In contrast, radar technology can overcome this shortcoming by offering a large detection volume, fully covering the rotor-swept areas of modern wind turbines. Our study focused on the common noctule bats (Nyctalus noctula). The measurement setup consisted of a portable X-band pulse radar with a modified radar antenna, a clutter shielding fence, and an acoustic bat detector installed in the wind turbine's nacelle. The radar's detection range was evaluated using an analytical simulation model. We developed a methodology based on a strict set of criteria for selecting suitable radar data, acoustic data and identified bat tracks. By applying this methodology, the study data was limited to time intervals with an average duration of 48 s, which is equal to approximately 20 radar images. For these time intervals, 323 bat tracks were identified. The most common bat speed was extracted to be between 9 and 10 m/s, matching the values found in the literature. Of the 323 identified bat tracks passed within 80 m of the acoustic detector, 32% had the potential to be associated with bat calls due to their timing, directionality, and distance to the acoustic bat detector. The remaining 68% passed within the studied radar detection volume but out of the detection volume of the acoustic bat detector. A comparison of recorded radar echoes with the expected simulated values indicated that the in-flight radar cross-section of recorded common noctule bats was mostly between 1.0 and 5.0 cm2, which is consistent with the values found in the literature for similar sized wildlife.

Optical Coherence Tomography Angiography-Navigated Laser Photocoagulation of Retinal Hemangioblastomas in Patients With von Hippel-Lindau Disease.

Purpose: To describe optical coherence tomography angiography (OCTA)-guided navigated laser photocoagulation (LP) using the Navilas Laser System for treating retinal hemangioblastomas (RHs) associated with von Hippel-Lindau disease (VHLD). Methods: Patients with VHLD were screened using ophthalmoscopy and widefield OCTA. Detected RHs were classified with regard to tumor morphology (endophytic, sessile, exophytic, recurrent) and size. Then, 6 × 6- or 3 × 3-mm2 en face OCTA scans of the RHs were uploaded to the Navilas system, generating a merged image combining the scan and Navilas fundus photography. LP was planned by placing laser spots in the OCTA scan and executed with the Navilas system. Treatment efficacy was assessed by conducting OCTA scans immediately after LP and at follow-up visits. Results: Fifteen RHs were detected in 10 patients (median, one RH; range, one to four). Twelve RHs were treatment naive (exophytic [3], sessile [3], and endophytic [6]), and there were three recurrent RHs in pretreated areas. Total applied energy per tumor correlated with tumor size (P < 0.001). After a mean first follow-up of 3.6 ± 1.5 months (range, 0.9-5.3), nine RHs exhibited complete regression (60%), five partial regression (33.3%), and one no regression (6.7%). No correlation between tumor morphology and treatment success was observed (P = 0.32). However, a correlation between treatment success and tumor size trended toward significance (P = 0.08), with a 100% success rate observed for small RHs. Conclusions: OCTA-guided LP via the Navilas Laser System is a promising technique, especially beneficial for targeting small RHs. Combining OCTA and ophthalmoscopy improves tumor detection, underscoring the utility of this approach. Translational Relevance: OCTA-guided LP enables highly precise and safe treatment of early-stage RHs, minimizing possible complications caused by LP or the tumor itself.

ZEISS PLEX Elite 9000 Widefield Optical Coherence Tomography Angiography as Screening Method for Early Detection of Retinal Hemangioblastomas in von Hippel-Lindau Disease.

Purpose: To evaluate early detection of retinal hemangioblastomas (RHs) in von Hippel-Lindau disease (VHLD) with widefield optical coherence tomography angiography (wOCTA) compared to the standard of care in ophthalmologic VHLD screening in a routine clinical setting. Methods: We conducted prospective comparisons of three screening methods: wOCTA, standard ophthalmoscopy, and fluorescein angiography (FA), which was performed only in uncertain cases. The numbers of detected RHs were compared among the three screening methods. The underlying causes for the lack of detection were investigated. Results: In 91 eyes (48 patients), 67 RHs were observed (mean, 0.74 ± 1.59 RH per eye). FA was performed in eight eyes. Ophthalmoscopy overlooked 25 of the 35 RHs detected by wOCTA (71.4%) due to the background color of the choroid (n = 5), small tumor size (n = 13), masking by a bright fundus reflex (n = 2), and masking by surrounding retinal scars (n = 5). However, wOCTA missed 29 RHs due to peripheral location (43.3%). The overall detection rates were up to 37% on the basis of ophthalmoscopy alone, up to 52% for wOCTA, and 89% for FA. Within the retinal area covered by wOCTA, the detection rates were up to 46.7% for ophthalmoscopy alone, up to 92.1% for wOCTA, and 73.3% for FA. Conclusions: The overall low detection rate of RHs using wOCTA is almost exclusively caused by its inability to visualize the entire peripheral retina. Therefore, in unclear cases, FA is necessary after ophthalmoscopy. Translational Relevance: Within the imageable retinal area, wOCTA shows a high detection rate of RHs and therefore may be suitable to improve screening for RHs in VHLD.

Simulation training on respectful emergency obstetric and neonatal care in north-western Madagascar: a mixed-methods evaluation of an innovative training program.

BACKGROUND: The rates of maternal and neonatal deaths in Madagascar are among the highest in the world. In response to a request for additional training from obstetrical care providers at the Ambanja district hospital in north-eastern Madagascar, a partnership of institutions in Switzerland and Madagascar conducted innovative training on respectful emergency obstetric and newborn care using e-learning and simulation methodologies. The training focused on six topics: pre-eclampsia, physiological childbirth, obstetric maneuvers, postpartum hemorrhage, maternal sepsis, and newborn resuscitation. Cross-cutting themes were interprofessional communication and respectful patient care. Ten experienced trainers participated in an e-training-of-trainers course conducted by the Swiss partners. The newly-trained trainers and Swiss partners then jointly conducted the hybrid remote/in-person training for 11 obstetrical care providers in Ambanja. METHODS: A mixed methods evaluation was conducted of the impact of the training on participants' knowledge and practices. Trainees' knowledge was tested before, immediately after, and 6 months after the training. Focus group discussions were conducted to elicit participants' opinions about the training, including the content and pedagogical methods. RESULTS: Trainees' knowledge of the six topics was higher at 6 months (with an average of 71% correct answers) compared to before the training (62%), although it was even higher (83%) immediately after the training. During the focus group discussions, participants highlighted their positive impressions of the training, including its impact on their sense of professional effectiveness. They reported that their interprofessional relationships and focus on respectful care had improved. Simulation, which was a new methodology for the participants native to Madagascar, was appreciated for its engaging and active format, and they enjoyed the hybrid delivery of the training. Participants (including the trainers) expressed a desire for follow-up engagement, including additional training, and improved access to more equipment. CONCLUSION: The evaluation showed improvements in trainees' knowledge and capacity to provide respectful emergency care to pregnant women and newborns across all training topics. The hybrid simulation-based training method elicited strong enthusiasm. Significant opportunity exists to expand the use of hybrid onsite/remote simulation-based training to improve obstetrical care and health outcomes for women and newborns in Madagascar and elsewhere.

Uncovering patterns of inhaler technique and reliever use: the value of objective, personalized data from a digital inhaler.

Electronic inhalers provide information about patterns of routine inhaler use. During a 12-week study, 360 asthma patients using albuterol Digihaler generated 53,083 inhaler events that were retrospectively analyzed. A total of 41,528 (78%) of the recorded inhalation events were suitable for flow analysis (having a PIF ≥ 18 L/min and <120 L/min). Median PIF, inhalation volume, inhalation duration, and time to PIF for these events steadily decreased between the first and last 10 days of the study, by 5.1%, 12.6%, 15.9%, and 6.4%, respectively. Continuous short-acting beta2-agonist (SABA) overuse, defined as ≥2 SABA inhalations/week throughout the study period, was seen in 29% (n = 104) of patients. Of 260 patients with ≥1 instance of acute short-term SABA overuse, 55 (21%) had a confirmed exacerbation. Electronic recording of real-life inhaler use can capture valuable, objective information that could inform disease management and clinical decision-making.

Retinal vessel volume reference database derived from volume-rendered optical coherence tomography angiography.

Optical coherence tomography angiography (OCTA) enables three-dimensional reconstruction of the functional blood vessels in the retina. Therefore, it enables the quantification of 3D retinal vessel parameters such as surface area and vessel volume. In spite of the widespread use of OCTA, no representative volume-rendered vessel volume (VV) data are published to date. In this study, OCTA 3 × 3 mm macular cubes were processed with volume-rendering techniques to measure VV in 203 eyes from 107 healthy volunteers. Generalized linear models (GLM) were constructed to assess the impact of age, gender, visual acuity (VA), spherical equivalent (SE), and axial length (AL) on VV. Overall mean VV was 0.23 ± 0.05mm3. Age and axial length showed a negative correlation with VV. However, GLM model analysis found that AL exerted the most pronounced influence on VV. No statistically significant associations were identified between gender or between left and right eyes. This is the first study to assess 3D OCTA VV and its naturally occurring variations in a large series of healthy subjects. It offers novel insights into the characterization of normal retinal vascular anatomy in healthy individuals, contributing to a valuable reference for future research in this field.

NMF Clustering: Accessible NMF-based Clustering Utilizing GPU Acceleration.

Non-negative Matrix Factorization (NMF) is an algorithm that can reduce high dimensional datasets of tens of thousands of genes to a handful of metagenes which are biologically easier to interpret. Application of NMF on gene expression data has been limited by its computationally intensive nature, which hinders its use on large datasets such as single-cell RNA sequencing (scRNA-seq) count matrices. We have implemented NMF based clustering to run on high performance GPU compute nodes using CuPy, a GPU backed python library, and the Message Passing Interface (MPI). This reduces the computation time by up to three orders of magnitude and makes the NMF Clustering analysis of large RNA-Seq and scRNA-seq datasets practical. We have made the method freely available through the GenePattern gateway, which provides free public access to hundreds of tools for the analysis and visualization of multiple 'omic data types. Its web-based interface gives easy access to these tools and allows the creation of multi-step analysis pipelines on high performance computing (HPC) clusters that enable reproducible in silico research for non-programmers.

Separación de funciones en el Sistema de Protección Social en Salud, México 2009: avances y retos / Separation of functions in the System of Social Protection in Health, Mexico 2009: progress and challenges

OBJETIVO. Analizar los avances y retos de la separación de funciones en el Sistema de Protección Social en Salud en México. MATERIAL Y MÉTODOS. Investigación evaluativa realizada en 2009. Se incorporaron nueve entidades federativas y la Comisión Nacional de Protección Social en Salud. Se realizaron entrevistas semiestructuradas a informantes clave y análisis documental. RESULTADOS. El principal avance es la creación de los Regímenes Estatales de Protección Social en Salud (REPSS), con una función de intermediación entre los usuarios y los prestadores de servicios de salud. Éstos se constituyen como instancias del nivel estatal encargadas de administrar los recursos financieros y conformar y coordinar la red de prestación de servicios de atención médica. No obstante, la mayoría de los REPSS estudiados se encuentran en un estado de inercia que les impide cumplir adecuadamente con las funciones marcadas por la ley. CONCLUSIÓN. Persisten obstáculos normativos, técnicos, políticos y gerenciales para cumplir con la separación de funciones.

OBJECTIVE. To evaluate advancements and challenges in the separation of functions within Mexico's System of Social Protection in Health. MATERIAL AND METHODS. A 2009 evaluation study involving nine states and the National Commission for Social Protection in Health was carried out via semi-structured interviews with key actors and literature analysis. RESULTS. The main advancement has been the creation of the State Regimens for Social Protection in Health (REPSS in Spanish) which act as intermediaries between users and health service providers, making these state-level entities responsible for both managing financial resources and shaping and coordinating the health care delivery network. However, most of the REPSS studied were found to be in a state of inertia, leading to inadequate compliance with legally mandated functions. CONCLUSION. Normative, technical, political and managerial obstacles persist, impeding the successful separation of functions.

Medicines in Mexico, 1990-2004: systematic review of research on access and use: [review] / Medicamentos en México, 1990-2004: revisión de investigación sobre acceso y uso: [revisión]

OBJECTIVE: To review original research studies published between 1990 and 2004 on the access and use of medicines in Mexico to assess the knowledge base for reforming Mexico's pharmaceutical policy. MATERIAL AND METHODS: A literature review using electronic databases was conducted of original studies published in the last 15 years about access and use of medicines in Mexico. In addition, a manual search of six relevant journals was performed. Excluded were publications on herbal, complementary and alternative medicines. RESULTS: Were identified 108 original articles as being relevant, out of 2289 titles reviewed, highlighting four policy-related problems: irrational prescribing, harmful self-medication, inequitable access, and frequent drug stock shortage in public health centers. CONCLUSIONS: This review identified two priorities for Mexico's pharmaceutical policy and strategies: tackling the irrational use of medicines and the inadequate access of medicines. These are critical priorities for a new national pharmaceutical policy.

OBJETIVO: Revisar estudios de investigaciones originales publicados sobre el acceso y uso de los medicamentos en México de 1990 a 2004, con el fin de evaluar el conocimiento que existe para reformar la política farmacéutica nacional. MATERIAL Y MÉTODOS: Se condujo una revisión de la literatura sobre estudios originales publicados entre 1990 y 2004 sobre el acceso y uso de medicamentos en México. Además, se revisaron manualmente seis revistas relevantes. Se excluyeron publicaciones sobre herbolaria, medicamentos tradicionales y alternativos. RESULTADOS: Se revisaron 2 289 artículos e identificaron 108 como relevantes que destacan cuatro problemas importantes relacionados con las políticas farmacéuticas: prescripción inadecuada, automedicación dañina, acceso inequitativo y desabasto de medicamentos en servicios públicos de salud. CONCLUSIONES: Esta revisión identificó dos prioridades críticas para el desarrollo de una nueva política farmacéutica en México: actuar sobre el uso irracional de medicamentos y sobre el acceso inadecuado a medicamentos.

El concepto y la práctica de la salud internacional en el Programa Takemi / The concept and practice of International healtah in the Takemi Program

El Programa Takemi en Salud Internacional se fundó en la Escuela de Salud Pública de Harvard en 1983 como un programa de investigación y capacitación al más alto nivel, dirigido a profesionales de la salud a mitad de su carrera e interesados en la distribución de recursos para la salud, particularmente en los países en desarrollo. Este ensayo describe los orígenes del Programa Takemi y presenta siete principios que subyacen en el concepto y la práctica de la salud internacional en él. Los principios son: énfasis en la investigación, orientación de las políticas, perspectiva interdisciplinaria, respeto mutuo, libertad individual, espíritu comunitario y desarrollo de la capacidad individual. Las implicaciones más generales de estos principios se proponen para los actuales esfuerzos por redefinir el concepto de salud internacional

The Takemi Program in International Health was established at the Harvard School of Public Health in 1983 as a research and advanced training program for mid-career health professionals concerned with the allocation of resources for health, especially in developing countries. This essay describes the origins of the Takemi Program and presents seven principles that underlie the concept and practice of international health in the Takemi Program. The principles are: research emphasis, policy orientation, interdisciplinary perspective; mutual respect, individual freedom, community spirit, and individual capacity building. The broader implications of these principles are suggested for current efforts to redefine the concept of international health.