I am sure that many of you have already seen this study which is currently an Article in Press in the British Journal of Sports Medicine.
Whilst I have great respect for the authors and team involved, I am going out on a limb to say that I consider the title and conclusions of the paper highly misleading and potentially dangerous for the running public and the evidence base. I never like to see a controlled trial with a statement as the title, and this is a great example as to why.
Take Your Shoes off to Reduce Patellofemoral Stress When Running
Aim: Elevated patellofemoral joint stress is thought to contribute to the development and progression of patellofemoral pain syndrome. The purpose of this study was to determine if running barefoot decreases patellofemoral joint stress in comparison to shod running.
Methods: Lower extremity kinematics and ground reaction force data were collected from 22 trained runners during overground running while barefoot and in a neutral running shoe. The kinematic and kinetic data were used as input variables into a previously described mathematical model to determine patellofemoral joint stress. Knee flexion angle, net knee extension moment and the model outputs of contact area, patellofemoral joint reaction force and patellofemoral joint stress were plotted over the stance phase of the gait cycle and peak values compared using paired t tests and standardised mean differences calculated.
Results: Running barefoot decreased peak patellofemoral joint stress by 12% (p=0.000) in comparison to shod running. The reduction in patellofemoral joint stress was a result of reduced patellofemoral joint reaction forces (12%, p=0.000) while running barefoot.
Conclusions: Elevated patellofemoral joint stress during shod running might contribute to patellofemoral pain. Running barefoot decreases patellofemoral joint stress.
Original Source 
Yes, when comparing shod versus Barefoot runners in this study, peak Patellofemoral Joint Stress was 12% lower in the Barefoot Group, which was statistically significant. However, other kinematic variables were also significantly different, including stride length reduction (2.4%), stride cadence increase (2%), ankle dorsiflexion in mid-stance reduction (82%) and knee flexion angle in mid-stance change (4.2% higher in the shod group). This highlights the importance of reading and appraising a paper and not making do with the abstract.
This is where I consider the conclusions of this paper to be misleading. In my opinion (and with several colleagues in agreement), it is the change in these kinematic variables, as opposed to the removal of running shoes, that will have lead to the reduction in Patellofemoral Joint Stress.
As always, I am not interested in opinion; you must back up your argument with high quality evidence. So here it is:
Increasing Running Step Rate Reduces Patellofemoral Joint Forces
Purpose: Increasing step rate has been shown to elicit changes in joint kinematics and kinetics during running, and has been suggested as a possible rehabilitation strategy for runners with patellofemoral pain. The purpose of this study was to determine how altering step rate affects internal muscle forces and patellofemoral joint loads, and then to determine what kinematic and kinetic factors best predict changes in joint loading.
Methods: We recorded whole body kinematics of 30 healthy adults running on an instrumented treadmill at three step rate conditions (90%, 100%, and 110% of preferred step rate). We then used a 3D lower extremity musculoskeletal model to estimate muscle, patellar tendon, and patellofemoral joint forces throughout the running gait cycles. Additionally, linear regression analysis allowed us to ascertain the relative influence of limb posture and external loads on patellofemoral joint force.
Results: Increasing step rate to 110% of preferred reduced peak patellofemoral joint force by 14%. Peak muscle forces were also altered as a result of the increased step rate with hip, knee and ankle extensor forces, and hip abductor forces all reduced in mid-stance. Compared to the 90% step rate condition, there was a concomitant increase in peak rectus femoris and hamstring loads during early and late swing, respectively, at higher step rates. Peak stance phase knee flexion decreased with increasing step rate, and was found to be the most important predictor of the reduction in patellofemoral joint loading.
Conclusion: Increasing step rate is an effective strategy to reduce patellofemoral joint forces and could be effective in modulating biomechanical factors that can contribute to patellofemoral pain.
Original Source 
This paper identifies that a higher stride cadence, reduced stride length and thus reduced knee Flexion angle at mid-stance significantly reduces Patellofemoral Joint loading (14%), without manipulating the variable of footwear. We must however remember that both of these studies involved healthy runners and not subjects with Patellofemoral pain and we should exercise care when applying this data to this subgroup of patients.
That being said, Noehren et al (2011) in BJSM proved that gait reeducation has a positive effect on subjects with Patellofemoral Pain and others have shown the positive effects that changing running biomechanics can have on joint loading as a whole (Brindle et al, 2013 & Heiderschiet et al, 2011 ). I expect there will be more studies along this route in the near future.
In conclusion, I think this study has a lot to offer the evidence base, just not in the fashion that the authors have concluded. Whilst I concede that removing footwear may be a way of inciting kinematic change when running, you can do it just as effectively with video analysis, metronomes, verbal cueing and functional drills. If you think that the cushioning or heel drop of your footwear is affecting your ability to initiate foot strike under your centre of mass, then you should strengthen your Gluteus Maximus and Hamstrings and improve your posture, dynamic pelvic positioning and swing phase mechanics, to start with.
So for now, clinicians and runners alike, don’t be duped into jumping on the barefoot bandwagon! Exercise some logic, as a middle ground of conscious gait reeducation and low-drop footwear is often more than adequate as a key part of the Patellofemoral rehab process.
 Bonacci et al (2013). Take your shoes off to reduce patellofemoral joint stress during running. BJSM. Article in Press.
 Bribdle et al (2013). Changing step width alters lower extremity biomechanics during running. Gait & Posture. Article in Press.
 Heiderscheit et al (2011). Effects of step rate manipulation on joint mechanics during running. Med Sci Sport Ex 43 (2), 296-302.
 Lenhart et al (2013). Increasing running step rate reduces patellofemoral joint forces. Med Sci Sport Ex. Article in Press.
 Noehren et al (2011). The effects of real-time gait retraining on hip kinematics, pain and function in subjects with patellofemoral pain syndrome. BJSM 45 691-696.